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/**
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* Copyright (C) 2019 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.pesi.validate;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Timestamp;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.app.common.PesiDestinations;
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import eu.etaxonomy.cdm.app.common.PesiSources;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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/**
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* Tests the ERMS -> PESI pipeline by comparing the source DB with destination PESI DB.
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*
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* @author a.mueller
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* @since 01.09.2019
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*/
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public class PesiErmsValidator {
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private static final Logger logger = Logger.getLogger(PesiErmsValidator.class);
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private static final Source defaultSource = PesiSources.PESI2019_ERMS_2019();
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private static final Source defaultDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI();
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// private static final Source defaultDestination = PesiDestinations.pesi_test_local_CDM_ERMS2PESI_2();
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private Source source = defaultSource;
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private Source destination = defaultDestination;
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private String moneraFilter = " NOT IN (-1)"; // 147415;
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// private String moneraFilter = " NOT IN (147415)"; // 147415;
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private String origErms = "OriginalDB = 'ERMS' ";
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public void invoke(Source source, Source destination){
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logger.warn("Validate destination " + destination.getDatabase());
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boolean success = true;
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try {
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this.source = source;
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this.destination = destination;
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// success &= testReferences(); //ready, few minor issues to be discussed with VLIZ
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success &= testTaxa();
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// success &= testTaxonRelations(); //name relations count!, single record compare tests for synonyms and included in
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// success &= testCommonNames(); //source(s) discuss VLIZ, exact duplicates (except for sources), Anus(Korur)
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// success &= testDistributions(); //>1000 duplicates in "dr", sources (OccurrenceSource table), 1 long note
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// success &= testNotes(); //ecology & link notes test (only count tested), sources untested (NoteSource table)
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// success &= testAdditionalTaxonSources(); //ready
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} catch (Exception e) {
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e.printStackTrace();
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success = false;
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}
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System.out.println("end validation " + (success? "":"NOT ") + "successful.");
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}
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private boolean testAdditionalTaxonSources() throws SQLException {
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System.out.println("Start validate additional taxon sources");
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boolean success = testAdditionalTaxonSourcesCount();
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if (success){
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success &= testSingleAdditionalTaxonSources(source.getUniqueInteger(countAddtionalTaxonSource));
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}
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return success;
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}
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private boolean testNotes() throws SQLException {
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System.out.println("Start validate notes");
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boolean success = testNotesCount();
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if (success){
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success &= testSingleNotes(source.getUniqueInteger("SELECT count(*) FROM notes "));
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}
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return success;
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}
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private boolean testDistributions() throws SQLException {
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System.out.println("Start validate distributions");
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boolean success = testDistributionCount();
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if (success){
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success &= testSingleDistributions(source.getUniqueInteger("SELECT count(*) FROM dr "));
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}
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return success;
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}
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private boolean testCommonNames() throws SQLException {
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System.out.println("Start validate common names");
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boolean success = testCommonNameCount();
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if (success){
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success &= testSingleCommonNames(source.getUniqueInteger("SELECT count(*) FROM vernaculars "));
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}
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return success;
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}
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int countSynonyms;
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int countIncludedIns;
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private boolean testTaxonRelations() throws SQLException {
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System.out.println("Start validate taxon relations");
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boolean success = testSynonymRelations(); //only count, single record test still missing
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success &= testIncludedInRelations(); //only count, single record test still missing
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success &= testTotalRelations();
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success &= testNameRelations();
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return success;
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}
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private boolean testTotalRelations() {
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if (!(countSynonyms < 0 || countIncludedIns < 0)){
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int countTotalSrc = countSynonyms + countIncludedIns;
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int countSrc = source.getUniqueInteger("SELECT count(*) FROM tu ");
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boolean success = equals("Taxrel count + 1 must be same as source taxon count ", countTotalSrc+1, countSrc, String.valueOf(-1));
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM Taxon t WHERE t."+ origErms);
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success &= equals("Taxrel count + 1 must be same as destination taxon count ", countTotalSrc+1, countDest, String.valueOf(-1));
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return success;
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}else{
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return false;
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}
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}
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private boolean testSynonymRelations() throws SQLException {
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int countSrc = source.getUniqueInteger(countSynonymRelation);
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM RelTaxon WHERE RelTaxonQualifierFk > 101");
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boolean success = equals("Synonym count ", countSrc, countDest, String.valueOf(-1));
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// update Match_RelStat set RelTaxon = 102 where tu_unacceptreason like 'currently placed%'
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// update Match_RelStat set RelTaxon = 102 where tu_unacceptreason like 'currently held%'
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// update Match_RelStat set RelTaxon = 102 where tu_unacceptreason like 'sy%' or tu_unacceptreason like '%jun%syn%'
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// update Match_RelStat set RelTaxon = 102 where tu_unacceptreason = '(synonym)'
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// update Match_RelStat set RelTaxon = 102 where tu_unacceptreason = 'reverted genus transfer'
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// update Match_RelStat set RelTaxon = 103 where tu_unacceptreason like 'misapplied%'
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// update Match_RelStat set RelTaxon = 104 where tu_unacceptreason like 'part% synonym%'
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// update Match_RelStat set RelTaxon = 106 where tu_unacceptreason = 'heterotypic synonym' or tu_unacceptreason = 'subjective synonym'
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// update Match_RelStat set RelTaxon = 107 where tu_unacceptreason like '%homot%syn%' or tu_unacceptreason = 'objective synonym' synyonym
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// update Match_RelStat set RelTaxon = 107 where tu_unacceptreason like '%bas[iy][no]%ny%'
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if (success){
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//TODO test single synonym relations
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// success &= testSingleTaxonRelations(source.getUniqueInteger(countSynonymRelation));
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}
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countSynonyms = (countSrc == countDest)? countSrc : -1;
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return success;
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}
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private boolean testNameRelations() {
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//Name relations
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int countSrc = source.getUniqueInteger("SELECT count(*) FROM tu WHERE id " + moneraFilter + " AND ("
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+ " tu_unacceptreason like '%bas[iy][no]%ny%' OR tu_unacceptreason = 'original combination' "
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+ " OR tu_unacceptreason = 'Subsequent combination' OR tu_unacceptreason like '%genus transfer%' "
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+ " OR tu_unacceptreason = 'genus change' " //1
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+ " OR tu_unacceptreason like '%homon%' " // 2
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+ " OR tu_unacceptreason like '%spell%' OR tu_unacceptreason like 'lapsus %' " //16
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+ ")");
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM RelTaxon WHERE RelTaxonQualifierFk <100 ");
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boolean success = equals("Taxon name relation count ", countSrc, countDest, String.valueOf(-1));
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if (success){
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//TODO test single name relation
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// success &= testSingleTaxonRelations(source.getUniqueInteger(countSynonymRelation));
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}
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return success;
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}
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private boolean testIncludedInRelations() {
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int countSrc = source.getUniqueInteger(countParentRelation);
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM RelTaxon WHERE RelTaxonQualifierFk = 101 ");
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boolean success = equals("Tax included in count ", countSrc, countDest, String.valueOf(-1));
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if (success){
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//TODO test single includedIn relations
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// success &= testSingleTaxonRelations(source.getUniqueInteger(countSynonymRelation));
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}
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countIncludedIns = (countSrc == countDest)? countSrc : -1;
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return success;
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}
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private boolean testTaxa() throws SQLException {
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System.out.println("Start validate taxa");
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boolean success = testTaxaCount();
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//FIXME
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if (!success){
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success &= testSingleTaxa(source.getUniqueInteger(countTaxon));
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}
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return success;
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}
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private boolean testReferences() throws SQLException {
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System.out.println("Start validate references");
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boolean success = testReferenceCount();
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if (success){
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success &= testSingleReferences();
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}
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return success;
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}
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private final String countAddtionalTaxonSource = "SELECT count(*) FROM tu_sources ts WHERE ts.tu_id " + moneraFilter;
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private boolean testAdditionalTaxonSourcesCount() {
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int countSrc = source.getUniqueInteger(countAddtionalTaxonSource);
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM AdditionalTaxonSource ");
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return equals("AdditionalTaxonSource count ", countSrc, countDest, String.valueOf(-1));
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}
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private boolean testNotesCount() {
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int countSrc = source.getUniqueInteger("SELECT count(*) FROM notes ");
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM Note "
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+ " WHERE NOT (NoteCategoryFk = 4 AND LastAction IS NULL) AND NOT NoteCategoryFk IN (22,23,24) ");
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boolean result = equals("Notes count ", countSrc, countDest, String.valueOf(-1));
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countSrc = source.getUniqueInteger("SELECT count(*) FROM tu "
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+ " WHERE (tu_marine IS NOT NULL OR tu_brackish IS NOT NULL OR tu_fresh IS NOT NULL OR tu_terrestrial IS NOT NULL) "
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+ " AND tu.id " + moneraFilter );
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countDest = destination.getUniqueInteger("SELECT count(*) FROM Note "
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+ " WHERE (NoteCategoryFk = 4 AND LastAction IS NULL) ");
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result &= equals("Notes ecology count ", countSrc, countDest, String.valueOf(-1));
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countSrc = source.getUniqueInteger("SELECT count(*) FROM links ");
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countDest = destination.getUniqueInteger("SELECT count(*) FROM Note "
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+ " WHERE NoteCategoryFk IN (22,23,24) ");
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result &= equals("Notes link count ", countSrc, countDest, String.valueOf(-1));
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return result;
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}
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private boolean testDistributionCount() {
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int countSrc = source.getUniqueInteger("SELECT count(*) FROM dr ");
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM Occurrence ");
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return equals("Occurrence count ", countSrc, countDest, String.valueOf(-1));
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}
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private boolean testCommonNameCount() {
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int countSrc = source.getUniqueInteger("SELECT count(*) FROM vernaculars ");
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM CommonName ");
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return equals("CommonName count ", countSrc, countDest, String.valueOf(-1));
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}
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private final String countSynonymRelation = "SELECT count(*) FROM tu syn LEFT JOIN tu acc ON syn.tu_accfinal = acc.id WHERE (syn.id <> acc.id AND syn.tu_accfinal IS NOT NULL AND syn.id <> acc.tu_parent) AND syn.id " + moneraFilter;
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private final String countParentRelation = "SELECT count(*)-1 FROM tu syn LEFT JOIN tu acc ON syn.tu_accfinal = acc.id WHERE (syn.id = acc.id OR syn.tu_accfinal IS NULL OR syn.id = acc.tu_parent) AND syn.id " + moneraFilter;
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private final String countTaxon = "SELECT count(*) FROM tu WHERE id " + moneraFilter;
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private boolean testTaxaCount() {
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int countSrc = source.getUniqueInteger(countTaxon);
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int countDest = destination.getUniqueInteger("SELECT count(*) FROM Taxon ");
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boolean result = equals("Taxon count ", countSrc, countDest, String.valueOf(-1));
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//NomStatus
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countSrc = source.getUniqueInteger("SELECT count(*) FROM tu WHERE id " + moneraFilter + " AND ("
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+ " tu_unacceptreason like '%inval%' OR tu_unacceptreason like '%not val%' "
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+ " OR tu_unacceptreason like '%illeg%' OR tu_unacceptreason like '%nud%' "
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+ " OR tu_unacceptreason like '%rej.%' OR tu_unacceptreason like '%superfl%' "
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+ " OR tu_unacceptreason like '%Comb. nov%' OR tu_unacceptreason like '%New name%' "
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+ " OR tu_unacceptreason = 'new combination' "
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+ " OR tu_status IN (3,5,6,7,8) )");
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countDest = destination.getUniqueInteger("SELECT count(*) FROM Taxon WHERE NameStatusFk IS NOT NULL ");
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result = equals("Taxon name status count ", countSrc, countDest, String.valueOf(-1));
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return result;
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}
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private boolean testSingleTaxa(int n) throws SQLException {
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boolean success = true;
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ResultSet srcRS = source.getResultSet(""
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+ " SELECT t.*, pt.tu_name pt_name, pt.id pId, pt.tu_accfinal pAccId, "
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+ " acc.tu_sp as acc_sp, accP.id accPId, "
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+ " r.rank_name, st.status_name, "
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+ " type.tu_displayname typename, type.tu_authority typeauthor, "
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+ " fo.fossil_name, qs.qualitystatus_name "
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+ " FROM tu t "
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+ " LEFT JOIN tu as pt on t.tu_parent = pt.id "
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+ " LEFT JOIN (SELECT DISTINCT rank_id, rank_name FROM ranks WHERE NOT(rank_id = 30 AND rank_name = 'Phylum (Division)' OR rank_id = 40 AND rank_name = 'Subphylum (Subdivision)' OR rank_id = 122 AND rank_name='Subsection')) as r ON t.tu_rank = r.rank_id "
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+ " LEFT JOIN tu acc ON acc.id = t.tu_accfinal "
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+ " LEFT JOIN tu accP ON acc.tu_parent = accP.id "
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+ " LEFT JOIN status st ON st.status_id = t.tu_status "
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+ " LEFT JOIN tu type ON type.id = t.tu_typetaxon "
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+ " LEFT JOIN fossil fo ON t.tu_fossil = fo.fossil_id "
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+ " LEFT JOIN qualitystatus qs ON t.tu_qualitystatus = qs.id "
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+ " WHERE t.id " + moneraFilter
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+ " ORDER BY CAST(t.id as nvarchar(20)) ");
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ResultSet destRS = destination.getResultSet("SELECT t.*, "
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+ " pt.GenusOrUninomial p_GenusOrUninomial, pt.InfraGenericEpithet p_InfraGenericEpithet, pt.SpecificEpithet p_SpecificEpithet, "
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+ " pt.treeIndex pTreeIndex, pt.IdInSource pIdInSource, "
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+ " s.Name as sourceName, type.IdInSource typeSourceId, r.Rank "
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+ " FROM Taxon t "
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+ " LEFT JOIN Taxon pt ON pt.TaxonId = t.ParentTaxonFk "
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+ " LEFT JOIN Taxon type ON type.TaxonId = t.TypeNameFk "
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+ " LEFT JOIN Rank r ON r.RankId = t.RankFk AND r.KingdomId = t.KingdomFk "
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+ " LEFT JOIN Source s ON s.SourceId = t.SourceFk "
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+ " WHERE t."+ origErms
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+ " ORDER BY t.IdInSource");
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ResultSet srcRsLastAction = source.getResultSet(""
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+ " SELECT t.id, s.sessiondate, a.action_name, s.ExpertName "
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+ " FROM tu t "
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+ " LEFT OUTER JOIN tu_sessions MN ON t.id = MN.tu_id "
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+ " LEFT JOIN actions a ON a.id = MN.action_id "
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+ " LEFT JOIN sessions s ON s.id = MN.session_id "
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+ " ORDER BY CAST(t.id as nvarchar(20)), s.sessiondate DESC, a.id DESC ");
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int i = 0;
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while (srcRS.next() && destRS.next()){
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success &= testSingleTaxon(srcRS, destRS);
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success &= testLastAction(srcRsLastAction, destRS, String.valueOf(srcRS.getInt("id")), "Taxon");
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i++;
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}
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success &= equals("Taxon count for single compare", n, i, String.valueOf(-1));
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return success;
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}
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private boolean testSingleTaxon(ResultSet srcRS, ResultSet destRS) throws SQLException {
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String id = String.valueOf(srcRS.getInt("id"));
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//complete
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311
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boolean success = equals("Taxon ID", "tu_id: " + srcRS.getInt("id"), destRS.getString("IdInSource"), id);
|
|
312
|
success &= equals("Taxon source", "ERMS export for PESI", destRS.getString("sourceName"), id);
|
|
313
|
|
|
314
|
success &= compareKingdom("Taxon kingdom", srcRS, destRS, id);
|
|
315
|
success &= equals("Taxon rank fk", srcRS.getString("tu_rank"), destRS.getString("RankFk"), id);
|
|
316
|
success &= equals("Taxon rank cache", normalizeRank(srcRS.getString("rank_name"), srcRS, id), destRS.getString("Rank"), id);
|
|
317
|
success &= compareNameParts(srcRS, destRS, id);
|
|
318
|
|
|
319
|
success &= equals("Taxon websearchname", srcRS.getString("tu_displayname"), destRS.getString("WebSearchName"), id);
|
|
320
|
//in ERMS displayName and webShowName should be equal as we do not have a correctly formatted nom. ref.
|
|
321
|
// success &= equals("Taxon WebShowName", srcDisplayName(srcRS), destRS.getString("WebShowName"), id);
|
|
322
|
success &= equals("Taxon authority", srcRS.getString("tu_authority"), destRS.getString("AuthorString"), id);
|
|
323
|
// success &= equals("Taxon FullName", srcFullName(srcRS), destRS.getString("FullName"), id);
|
|
324
|
success &= isNull("NomRefString", destRS, id);
|
|
325
|
// success &= equals("Taxon DisplayName", srcDisplayName(srcRS), destRS.getString("DisplayName"), id); //according to SQL script same as FullName, no nom.ref. information attached
|
|
326
|
|
|
327
|
//TODO nameStatusFk success &= equals("Taxon NameStatusFk", toNameStatus(nullSafeInt(srcRS, "tu_status")),nullSafeInt( destRS,"NameStatusFk"), id);
|
|
328
|
//TODO nameStatusCache success &= equals("Taxon NameStatusCache", srcRS.getString("status_name"), destRS.getString("NameStatusCache"), id);
|
|
329
|
|
|
330
|
success &= equals("Taxon TaxonStatusFk", normalizeTaxonStatusFk(srcRS),nullSafeInt( destRS,"TaxonStatusFk"), id);
|
|
331
|
success &= equals("Taxon TaxonStatusCache", normalizeTaxonStatusCache(srcRS), destRS.getString("TaxonStatusCache"), id);
|
|
332
|
|
|
333
|
success &= equals("Taxon ParentTaxonFk", srcParentTaxonFk(srcRS), destParentIdInSource(destRS), id);
|
|
334
|
Integer orgigTypeNameFk = nullSafeInt(srcRS, "tu_typetaxon");
|
|
335
|
success &= equals("Taxon TypeNameFk", orgigTypeNameFk == null? null : "tu_id: " + orgigTypeNameFk, destRS.getString("typeSourceId"), id);
|
|
336
|
//TODO success &= equals("Taxon TypeFullNameCache", CdmUtils.concat(" ", srcRS.getString("typename"), srcRS.getString("typeauthor")), destRS.getString("TypeFullNameCache"), id);
|
|
337
|
success &= equals("Taxon QualityStatusFK", nullSafeInt(srcRS, "tu_qualitystatus"),nullSafeInt( destRS,"QualityStatusFk"), String.valueOf(id));
|
|
338
|
success &= equals("Taxon QualityStatusCache", srcRS.getString("qualitystatus_name"), destRS.getString("QualityStatusCache"), id);
|
|
339
|
//the >200 taxa having themselves as grandparents are currently still reported as errors (what they are but they are handled during im/export
|
|
340
|
// success &= testTreeIndex(destRS, "TreeIndex", "pTreeIndex", id);
|
|
341
|
success &= equals("Taxon FossilStatusFk", nullSafeInt(srcRS, "tu_fossil"),nullSafeInt( destRS,"FossilStatusFk"), String.valueOf(id));
|
|
342
|
success &= equals("Taxon FossilStatusCache", srcRS.getString("fossil_name"), destRS.getString("FossilStatusCache"), id);
|
|
343
|
success &= equals("Taxon GUID", srcRS.getString("GUID"), destRS.getString("GUID"), id);
|
|
344
|
success &= equals("Taxon DerivedFromGuid", srcRS.getString("GUID"), destRS.getString("DerivedFromGuid"), id); //according to SQL script GUID and DerivedFromGuid are always the same, according to 2014DB this is even true for all databases
|
|
345
|
success &= isNull("ExpertGUID", destRS, id); //only relevant after merge
|
|
346
|
success &= isNull("ExpertName", destRS, id); //only relevant after merge
|
|
347
|
success &= isNull("SpeciesExpertGUID", destRS, id); //only relevant after merge
|
|
348
|
success &= equals("Taxon cache citation", srcRS.getString("cache_citation"), destRS.getString("CacheCitation"), id);
|
|
349
|
//LastAction(Date) handled in separate method
|
|
350
|
success &= isNull("GUID2", destRS, id); //only relevant after merge
|
|
351
|
success &= isNull("DerivedFromGuid2", destRS, id); //only relevant after merge
|
|
352
|
return success;
|
|
353
|
}
|
|
354
|
|
|
355
|
private Integer destParentIdInSource(ResultSet destRS) throws SQLException {
|
|
356
|
String parentIdInSource = destRS.getString("pIdInSource");
|
|
357
|
if (parentIdInSource == null){
|
|
358
|
return null;
|
|
359
|
}else{
|
|
360
|
String idStr = parentIdInSource.replace("tu_id:", "").trim();
|
|
361
|
Integer result = Integer.valueOf(idStr);
|
|
362
|
return result;
|
|
363
|
}
|
|
364
|
}
|
|
365
|
|
|
366
|
private Integer srcParentTaxonFk(ResultSet srcRS) throws SQLException {
|
|
367
|
Integer id = nullSafeInt(srcRS,"id");
|
|
368
|
Integer accId = nullSafeInt(srcRS, "tu_accfinal");
|
|
369
|
Integer pId = nullSafeInt(srcRS, "pId");
|
|
370
|
Integer pAccId = nullSafeInt(srcRS, "pAccId");
|
|
371
|
Integer accPId = nullSafeInt(srcRS, "accPId"); //parent of accepted taxon
|
|
372
|
|
|
373
|
if (accId != null && !id.equals(accId)){
|
|
374
|
if (id.equals(accPId)){
|
|
375
|
return pId; //exceptional handling to avoid recursion mostly for some autonyms and alternate representations
|
|
376
|
}else{
|
|
377
|
return null; //taxon is not accepted
|
|
378
|
}
|
|
379
|
}else{
|
|
380
|
if (id == 1){
|
|
381
|
return null; //Biota
|
|
382
|
}else if (pAccId == null){
|
|
383
|
return pId; //handle parent preliminary as accepted
|
|
384
|
}else if (id.equals(pAccId)){
|
|
385
|
return pId; //exceptional handling to avoid recursion mostly for some autonyms and alternate representations
|
|
386
|
}else{
|
|
387
|
return pAccId;
|
|
388
|
}
|
|
389
|
}
|
|
390
|
}
|
|
391
|
|
|
392
|
private Integer normalizeTaxonStatusFk(ResultSet srcRS) throws SQLException {
|
|
393
|
int id = srcRS.getInt("id");
|
|
394
|
Integer accFinal = nullSafeInt(srcRS, "tu_accfinal");
|
|
395
|
boolean accFinalDiffers = accFinal != null && !accFinal.equals(id);
|
|
396
|
|
|
397
|
if (accFinalDiffers){
|
|
398
|
return PesiTransformer.T_STATUS_SYNONYM; //2
|
|
399
|
}else{
|
|
400
|
Integer status = nullSafeInt(srcRS, "tu_status");
|
|
401
|
if(status == 1){ //accepted
|
|
402
|
return PesiTransformer.T_STATUS_ACCEPTED;
|
|
403
|
}else if (status == 6 || status == 8 || status == 10){ //nomen dubium, taxon inquirendum (status uncertain), uncertain
|
|
404
|
return PesiTransformer.T_STATUS_UNRESOLVED;
|
|
405
|
}else if (status == 2 || status == 3 || status == 5 || status == 7 || status == 9){ //unaccepted, nomen nudum, alternate representation, temporary name, interim unpublished
|
|
406
|
return PesiTransformer.T_STATUS_UNACCEPTED;
|
|
407
|
}
|
|
408
|
}
|
|
409
|
//4 does not exist and should not happen
|
|
410
|
return -1;
|
|
411
|
}
|
|
412
|
|
|
413
|
private String normalizeTaxonStatusCache(ResultSet srcRS) throws SQLException {
|
|
414
|
Integer status = normalizeTaxonStatusFk(srcRS);
|
|
415
|
if (status == 1){
|
|
416
|
return "accepted";
|
|
417
|
}else if (status == 2){
|
|
418
|
return "synonym";
|
|
419
|
}else if (status == 4){
|
|
420
|
return "pro parte synonym";
|
|
421
|
}else if (status == 5){
|
|
422
|
return "unresolved";
|
|
423
|
}else if (status == 7){
|
|
424
|
return "unaccepted";
|
|
425
|
}else{
|
|
426
|
return "xxx - not yet handled";
|
|
427
|
}
|
|
428
|
}
|
|
429
|
|
|
430
|
private boolean testTreeIndex(ResultSet destRS, String childIndexAttr, String parentIndexAttr, String id) throws SQLException {
|
|
431
|
boolean result;
|
|
432
|
int taxonStatusFk = destRS.getInt("TaxonStatusFk");
|
|
433
|
String parentTaxonId = destRS.getString("parentTaxonFk");
|
|
434
|
int rankFk = destRS.getInt("RankFk");
|
|
435
|
if (taxonStatusFk == 2 || taxonStatusFk == 4 || rankFk <= 10){ //synonym; pro parte syn; kingdom and higher
|
|
436
|
result = isNull(childIndexAttr, destRS, id);
|
|
437
|
}else{
|
|
438
|
String childIndex = destRS.getString(childIndexAttr);
|
|
439
|
String parentIndex = destRS.getString(parentIndexAttr);
|
|
440
|
parentIndex = parentIndex == null? "#": parentIndex;
|
|
441
|
result = equals("Tree index", childIndex, parentIndex + parentTaxonId + "#", id);
|
|
442
|
}
|
|
443
|
return result;
|
|
444
|
}
|
|
445
|
|
|
446
|
boolean namePartsFirst = true;
|
|
447
|
private boolean compareNameParts(ResultSet srcRS, ResultSet destRS, String id) throws SQLException {
|
|
448
|
if (namePartsFirst){
|
|
449
|
logger.warn("Validation of name parts not fully implemented (difficult). Currently validated via fullname");
|
|
450
|
namePartsFirst = false;
|
|
451
|
}
|
|
452
|
int rankFk = srcRS.getInt("tu_rank");
|
|
453
|
String genusOrUninomial = null;
|
|
454
|
String infraGenericEpithet = null;
|
|
455
|
String specificEpithet = null;
|
|
456
|
String infraSpecificEpithet = null;
|
|
457
|
if (rankFk <= 180){
|
|
458
|
genusOrUninomial = srcRS.getString("tu_name");
|
|
459
|
}else if (rankFk == 190){
|
|
460
|
genusOrUninomial = srcRS.getString("pt_name");
|
|
461
|
infraGenericEpithet = srcRS.getString("tu_name");
|
|
462
|
//TODO compareNameParts does not work this way
|
|
463
|
// }else if (rankFk == 220){
|
|
464
|
// genusOrUninomial = destRS.getString("p_GenusOrUninomial");
|
|
465
|
// infraGenericEpithet = destRS.getString("p_InfraGenericEpithet");
|
|
466
|
// specificEpithet = srcRS.getString("tu_name");
|
|
467
|
}else{
|
|
468
|
//TODO exception (compare name parts)
|
|
469
|
return false;
|
|
470
|
}
|
|
471
|
boolean result = testEpis(destRS, genusOrUninomial, infraGenericEpithet,
|
|
472
|
specificEpithet, infraSpecificEpithet, id);
|
|
473
|
return result;
|
|
474
|
}
|
|
475
|
|
|
476
|
private boolean testEpis(ResultSet destRS, String genusOrUninomial, String infraGenericEpithet, String specificEpithet,
|
|
477
|
String infraSpecificEpithet, String id) throws SQLException {
|
|
478
|
boolean result = equals("Taxon genusOrUninomial", genusOrUninomial, destRS.getString("GenusOrUninomial"), id) ;
|
|
479
|
result &= equals("Taxon infraGenericEpithet", infraGenericEpithet, destRS.getString("InfraGenericEpithet"), id) ;
|
|
480
|
result &= equals("Taxon specificEpithet", specificEpithet, destRS.getString("SpecificEpithet"), id) ;
|
|
481
|
result &= equals("Taxon infraSpecificEpithet", infraSpecificEpithet, destRS.getString("InfraSpecificEpithet"), id) ;
|
|
482
|
return result;
|
|
483
|
}
|
|
484
|
|
|
485
|
private String normalizeRank(String string, ResultSet srcRS, String id) throws SQLException {
|
|
486
|
String result = string
|
|
487
|
.replace("Subforma", "Subform")
|
|
488
|
.replace("Forma", "Form");
|
|
489
|
int kingdomFk = Integer.valueOf(getSourceKingdomFk(srcRS, id));
|
|
490
|
if (kingdomFk == 3 || kingdomFk == 4){
|
|
491
|
result = result.replace("Subphylum", "Subdivision");
|
|
492
|
result = result.replace("Phylum", "Division");
|
|
493
|
}
|
|
494
|
return result;
|
|
495
|
}
|
|
496
|
|
|
497
|
//see also ErmsTaxonImport.getExpectedTitleCache()
|
|
498
|
private String srcFullName(ResultSet srcRs) throws SQLException {
|
|
499
|
String result = null;
|
|
500
|
String epi = srcRs.getString("tu_name");
|
|
501
|
String display = srcRs.getString("tu_displayname");
|
|
502
|
String sp = srcRs.getString("tu_sp");
|
|
503
|
if (display.indexOf(epi) != display.lastIndexOf(epi) && !sp.startsWith("#2#")){ //autonym, !animal
|
|
504
|
String authority = srcRs.getString("tu_authority");
|
|
505
|
result = srcRs.getString("tu_displayname").replaceFirst(epi+" ", CdmUtils.concat(" ", epi, authority)+" ");
|
|
506
|
}else{
|
|
507
|
result = CdmUtils.concat(" ", srcRs.getString("tu_displayname"), srcRs.getString("tu_authority"));
|
|
508
|
}
|
|
509
|
return result;
|
|
510
|
}
|
|
511
|
|
|
512
|
private String srcDisplayName(ResultSet srcRs) throws SQLException {
|
|
513
|
String result = null;
|
|
514
|
String epi = srcRs.getString("tu_name");
|
|
515
|
epi = " a" + epi;
|
|
516
|
String display = "<i>"+srcRs.getString("tu_displayname")+"</i>";
|
|
517
|
display = display.replace(" var. ", "</i> var. <i>").replace(" f. ", "</i> f. <i>");
|
|
518
|
String sp = srcRs.getString("tu_sp");
|
|
519
|
if (display.indexOf(epi) != display.lastIndexOf(epi) && !sp.startsWith("#2#")){ //homonym, animal
|
|
520
|
result = display.replaceFirst(epi+" ", CdmUtils.concat(" ", " "+epi, srcRs.getString("tu_authority")))+" ";
|
|
521
|
}else{
|
|
522
|
result = CdmUtils.concat(" ", display, srcRs.getString("tu_authority"));
|
|
523
|
}
|
|
524
|
return result;
|
|
525
|
}
|
|
526
|
|
|
527
|
String lastLastActionId = "-1";
|
|
528
|
private boolean testLastAction(ResultSet srcRsLastAction, ResultSet destRs, String id, String table) throws SQLException {
|
|
529
|
try {
|
|
530
|
boolean success = true;
|
|
531
|
String srcId = null;
|
|
532
|
while (srcRsLastAction.next()){
|
|
533
|
srcId = String.valueOf(srcRsLastAction.getInt("id"));
|
|
534
|
if (!lastLastActionId.equals(srcId)){
|
|
535
|
lastLastActionId = srcId;
|
|
536
|
break;
|
|
537
|
}
|
|
538
|
}
|
|
539
|
if(!id.equals(srcId)){
|
|
540
|
logger.warn("Last Action SourceIDs are not equal: id: " +id + ", la-id: " + srcId);
|
|
541
|
}
|
|
542
|
String destStr = destRs.getString("LastAction");
|
|
543
|
success &= equals(table + " SpeciesExpertName", srcRsLastAction.getString("ExpertName"), destRs.getString("SpeciesExpertName"), id); //mapping ExpertName => SpeciesExpertName according to SQL script
|
|
544
|
success &= equals(table + " Last Action", srcRsLastAction.getString("action_name"), destStr == null? null : destStr, id);
|
|
545
|
success &= equals(table + " Last Action Date", srcRsLastAction.getTimestamp("sessiondate"), destRs.getTimestamp("LastActionDate"), id);
|
|
546
|
|
|
547
|
return success;
|
|
548
|
} catch (Exception e) {
|
|
549
|
e.printStackTrace();
|
|
550
|
throw e;
|
|
551
|
}
|
|
552
|
}
|
|
553
|
|
|
554
|
private boolean compareKingdom(String messageStart, ResultSet srcRS, ResultSet destRS, String id) throws SQLException {
|
|
555
|
String srcKingdom = getSourceKingdomFk(srcRS, id);
|
|
556
|
Integer intDest = nullSafeInt(destRS, "KingdomFk");
|
|
557
|
if (intDest == null){
|
|
558
|
logger.warn(id +": " + messageStart + " must never be null for destination. Biota needs to be 0, all the rest needs to have >0 int value.");
|
|
559
|
return false;
|
|
560
|
}else{
|
|
561
|
return equals(messageStart, srcKingdom, String.valueOf(intDest), id);
|
|
562
|
}
|
|
563
|
}
|
|
564
|
|
|
565
|
private String getSourceKingdomFk(ResultSet srcRS, String id) throws SQLException {
|
|
566
|
String strSrc = srcRS.getString("acc_sp");
|
|
567
|
if (strSrc == null){
|
|
568
|
strSrc = srcRS.getString("tu_sp");
|
|
569
|
}
|
|
570
|
if (strSrc == null){
|
|
571
|
if ("1".equals(id)){
|
|
572
|
strSrc = "0"; //Biota
|
|
573
|
}else if ("147415".equals(id)){
|
|
574
|
strSrc = "6"; //Monera is synonym of Bacteria
|
|
575
|
}else{
|
|
576
|
strSrc = id;
|
|
577
|
}
|
|
578
|
}else{
|
|
579
|
strSrc = strSrc.substring(1);
|
|
580
|
strSrc = strSrc.substring(0, strSrc.indexOf("#"));
|
|
581
|
}
|
|
582
|
return strSrc;
|
|
583
|
}
|
|
584
|
|
|
585
|
private boolean testSingleTaxonRelations(int n) throws SQLException {
|
|
586
|
boolean success = true;
|
|
587
|
ResultSet srcRS = source.getResultSet(""
|
|
588
|
+ " SELECT t.* "
|
|
589
|
+ " FROM tu t "
|
|
590
|
+ " WHERE t.id "+ moneraFilter + " AND tu_accfinal <> id "
|
|
591
|
+ " ORDER BY CAST(t.id as nvarchar(20)) ");
|
|
592
|
ResultSet destRS = destination.getResultSet("SELECT rel.*, t1.IdInSource t1Id, t2.IdInSource t2Id "
|
|
593
|
+ " FROM RelTaxon rel "
|
|
594
|
+ " LEFT JOIN Taxon t1 ON t1.TaxonId = rel.TaxonFk1 "
|
|
595
|
+ " LEFT JOIN Taxon t2 ON t2.TaxonId = rel.TaxonFk2 "
|
|
596
|
+ " WHERE t1."+origErms+" AND t2." + origErms
|
|
597
|
+ " ORDER BY t1.IdInSource");
|
|
598
|
int i = 0;
|
|
599
|
while (srcRS.next() && destRS.next()){
|
|
600
|
success &= testSingleTaxonRelation(srcRS, destRS);
|
|
601
|
i++;
|
|
602
|
}
|
|
603
|
success &= equals("Taxon relation count for single compare", n, i, String.valueOf(-1));
|
|
604
|
return success;
|
|
605
|
}
|
|
606
|
|
|
607
|
private boolean testSingleTaxonRelation(ResultSet srcRS, ResultSet destRS) throws SQLException {
|
|
608
|
String id = String.valueOf(srcRS.getInt("id"));
|
|
609
|
boolean success = equals("Taxon relation taxon1", "tu_id: " + srcRS.getInt("id"), destRS.getString("t1Id"), id);
|
|
610
|
success &= equals("Taxon relation taxon2", "tu_id: " + srcRS.getInt("tu_accfinal"), destRS.getString("t2Id"), id);
|
|
611
|
success &= equals("Taxon relation qualifier fk", PesiTransformer.IS_SYNONYM_OF, destRS.getInt("RelTaxonQualifierFk"), id);
|
|
612
|
success &= equals("Taxon relation qualifier cache", "is synonym of", destRS.getString("RelQualifierCache"), id);
|
|
613
|
success &= isNull("notes", destRS, id);
|
|
614
|
//complete if no further relations need to be added
|
|
615
|
return success;
|
|
616
|
}
|
|
617
|
|
|
618
|
private boolean testSingleAdditionalTaxonSources(int n) throws SQLException {
|
|
619
|
boolean success = true;
|
|
620
|
ResultSet srcRs = source.getResultSet("SELECT CAST(tu.id as nvarchar(20)) tuId, MN.*, s.*, su.sourceuse_name "
|
|
621
|
+ " FROM tu_sources MN INNER JOIN tu ON MN.tu_id = tu.id "
|
|
622
|
+ " LEFT JOIN sources s ON s.id = MN.source_id "
|
|
623
|
+ " LEFT JOIN sourceuses su ON MN.sourceuse_id = su.sourceuse_id "
|
|
624
|
+ " WHERE MN.tu_id " + moneraFilter
|
|
625
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), MN.sourceuse_id, s.id "); //, no.note (not possible because ntext
|
|
626
|
ResultSet destRs = destination.getResultSet("SELECT t.IdInSource, ats.*, s.*, su.* "
|
|
627
|
+ " FROM AdditionalTaxonSource ats INNER JOIN Taxon t ON t.TaxonId = ats.TaxonFk "
|
|
628
|
+ " INNER JOIN Source s ON s.SourceId = ats.SourceFk "
|
|
629
|
+ " LEFT JOIN SourceUse su ON su.SourceUseId = ats.SourceUseFk "
|
|
630
|
+ " WHERE t."+origErms
|
|
631
|
+ " ORDER BY t.IdInSource, su.SourceUseId, s.RefIdInSource ");
|
|
632
|
int count = 0;
|
|
633
|
while (srcRs.next() && destRs.next()){
|
|
634
|
success &= testSingleAdditionalTaxonSource(srcRs, destRs);
|
|
635
|
count++;
|
|
636
|
}
|
|
637
|
success &= equals("Notes count differs", n, count, "-1");
|
|
638
|
return success;
|
|
639
|
}
|
|
640
|
|
|
641
|
private boolean testSingleAdditionalTaxonSource(ResultSet srcRs, ResultSet destRs) throws SQLException {
|
|
642
|
String id = String.valueOf(srcRs.getInt("tuId") + "-" + srcRs.getString("sourceuse_name"));
|
|
643
|
boolean success = equals("Additional taxon source taxonID ", "tu_id: " + String.valueOf(srcRs.getInt("tuId")), destRs.getString("IdInSource"), id);
|
|
644
|
success &= equals("Additional taxon source fk ", srcRs.getString("source_id"), destRs.getString("RefIdInSource"), id); //currently we use the same id in ERMS and PESI
|
|
645
|
success &= equals("Additional taxon source use fk ", srcRs.getString("sourceuse_id"), destRs.getString("SourceUseFk"), id);
|
|
646
|
success &= equals("Additional taxon source use cache ", srcRs.getString("sourceuse_name"), destRs.getString("SourceUseCache"), id);
|
|
647
|
//TODO some records are still truncated ~ >820 characters
|
|
648
|
success &= equals("Additional taxon source name cache ", srcRs.getString("source_name"), destRs.getString("SourceNameCache"), id);
|
|
649
|
success &= equals("Additional taxon source detail ", srcRs.getString("pagenr"), destRs.getString("SourceDetail"), id);
|
|
650
|
//Complete
|
|
651
|
return success;
|
|
652
|
}
|
|
653
|
|
|
654
|
private boolean testSingleNotes(int n) throws SQLException {
|
|
655
|
boolean success = true;
|
|
656
|
ResultSet srcRs = source.getResultSet("SELECT CAST(tu.id as nvarchar(20)) tuId, no.*, l.LanName "
|
|
657
|
+ " FROM notes no INNER JOIN tu ON no.tu_id = tu.id "
|
|
658
|
+ " LEFT JOIN languages l ON l.LanID = no.lan_id "
|
|
659
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), no.type, no.noteSortable "); //, no.note (not possible because ntext
|
|
660
|
ResultSet destRs = destination.getResultSet("SELECT t.IdInSource, no.*, cat.NoteCategory, l.Language "
|
|
661
|
+ " FROM Note no INNER JOIN Taxon t ON t.TaxonId = no.TaxonFk "
|
|
662
|
+ " LEFT JOIN NoteCategory cat ON cat.NoteCategoryId = no.NoteCategoryFk "
|
|
663
|
+ " LEFT JOIN Language l ON l.LanguageId = no.LanguageFk "
|
|
664
|
+ " WHERE t." + origErms
|
|
665
|
+ " AND NOT (NoteCategoryFk = 4 AND no.LastAction IS NULL) AND NOT NoteCategoryFk IN (22,23,24) "
|
|
666
|
+ " ORDER BY t.IdInSource, no.NoteCategoryCache, Note_1 ");
|
|
667
|
int count = 0;
|
|
668
|
ResultSet srcRsLastAction = source.getResultSet(""
|
|
669
|
+ " SELECT no.id, s.sessiondate, a.action_name, s.ExpertName "
|
|
670
|
+ " FROM notes no "
|
|
671
|
+ " INNER JOIN tu ON tu.id = no.tu_id "
|
|
672
|
+ " LEFT JOIN languages l ON l.LanID = no.lan_id"
|
|
673
|
+ " LEFT JOIN notes_sessions MN ON no.id = MN.note_id "
|
|
674
|
+ " LEFT JOIN actions a ON a.id = MN.action_id "
|
|
675
|
+ " LEFT JOIN sessions s ON s.id = MN.session_id "
|
|
676
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), no.type, no.noteSortable, s.sessiondate DESC, a.id DESC ");
|
|
677
|
|
|
678
|
while (srcRs.next() && destRs.next()){
|
|
679
|
success &= testSingleNote(srcRs, destRs);
|
|
680
|
success &= testLastAction(srcRsLastAction, destRs, String.valueOf(srcRs.getInt("id")), "Note");
|
|
681
|
count++;
|
|
682
|
}
|
|
683
|
success &= equals("Notes count differs", n, count, "-1");
|
|
684
|
return success;
|
|
685
|
}
|
|
686
|
|
|
687
|
private boolean testSingleNote(ResultSet srcRs, ResultSet destRs) throws SQLException {
|
|
688
|
String id = String.valueOf(srcRs.getInt("tuId") + "-" + srcRs.getString("type"));
|
|
689
|
boolean success = equals("Note taxonID ", "tu_id: " + String.valueOf(srcRs.getInt("tuId")), destRs.getString("IdInSource"), id);
|
|
690
|
success &= equals("Note Note_1 ", srcRs.getString("note"), destRs.getString("Note_1"), id);
|
|
691
|
success &= isNull("Note_2", destRs, id);
|
|
692
|
success &= equals("Note category cache", normalizeNoteCatCache(srcRs.getString("type")), destRs.getString("NoteCategoryCache"), id);
|
|
693
|
success &= equals("Note language ", srcRs.getString("LanName"), destRs.getString("Language"), id);
|
|
694
|
success &= isNull("Region", destRs, id);
|
|
695
|
success &= isNull("SpeciesExpertGUID", destRs, id);
|
|
696
|
//SpeciesExpertName, LastAction, LastActionDate handled in separate method
|
|
697
|
//complete
|
|
698
|
return success;
|
|
699
|
}
|
|
700
|
|
|
701
|
private String normalizeNoteCatCache(String string) {
|
|
702
|
return StringUtils.capitalize(string)
|
|
703
|
.replace("Original Combination", "Original combination")
|
|
704
|
.replace("Taxonomic remark", "Taxonomic Remark");
|
|
705
|
}
|
|
706
|
|
|
707
|
private boolean testSingleDistributions(int n) throws SQLException {
|
|
708
|
boolean success = true;
|
|
709
|
ResultSet srcRs = source.getResultSet("SELECT CAST(ISNULL(tu.tu_accfinal, tu.id) as nvarchar(20)) tuId,"
|
|
710
|
+ " gu.gazetteer_id, dr.*, gu.id guId, gu.gu_name "
|
|
711
|
+ " FROM dr INNER JOIN tu ON dr.tu_id = tu.id "
|
|
712
|
+ " LEFT JOIN gu ON gu.id = dr.gu_id "
|
|
713
|
+ " ORDER BY CAST(ISNULL(tu.tu_accfinal, tu.id) as nvarchar(20)), gu.gazetteer_id, gu.gu_name, dr.noteSortable "); //, dr.note (not possible because ntext
|
|
714
|
ResultSet destRs = destination.getResultSet("SELECT t.IdInSource, a.AreaERMSGazetteerId, oc.*, a.AreaName "
|
|
715
|
+ " FROM Occurrence oc INNER JOIN Taxon t ON t.TaxonId = oc.TaxonFk "
|
|
716
|
+ " LEFT JOIN Area a ON a.AreaId = oc.AreaFk "
|
|
717
|
+ " WHERE t." + origErms
|
|
718
|
+ " ORDER BY t.IdInSource, a.AreaERMSGazetteerId, a.AreaName, oc.Notes ");
|
|
719
|
ResultSet srcRsLastAction = source.getResultSet(""
|
|
720
|
+ " SELECT dr.id, s.sessiondate, a.action_name, s.ExpertName "
|
|
721
|
+ " FROM dr "
|
|
722
|
+ " INNER JOIN tu ON tu.id = dr.tu_id "
|
|
723
|
+ " LEFT JOIN gu ON gu.id = dr.gu_id "
|
|
724
|
+ " LEFT JOIN dr_sessions MN ON dr.id = MN.dr_id "
|
|
725
|
+ " LEFT JOIN actions a ON a.id = MN.action_id "
|
|
726
|
+ " LEFT JOIN sessions s ON s.id = MN.session_id "
|
|
727
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), gu.gazetteer_id, gu.gu_name, s.sessiondate DESC, a.id DESC ");
|
|
728
|
int count = 0;
|
|
729
|
while (srcRs.next() && destRs.next()){
|
|
730
|
success &= testSingleDistribution(srcRs, destRs);
|
|
731
|
//there are >1000 duplicates in dr, therefore this creates lots of warnings
|
|
732
|
success &= testLastAction(srcRsLastAction, destRs, String.valueOf(srcRs.getInt("id")), "Distribution");
|
|
733
|
count++;
|
|
734
|
}
|
|
735
|
success &= equals("Distribution count differs", n, count, "-1");
|
|
736
|
return success;
|
|
737
|
}
|
|
738
|
|
|
739
|
private boolean testSingleDistribution(ResultSet srcRs, ResultSet destRs) throws SQLException {
|
|
740
|
String id = String.valueOf(srcRs.getInt("tuId") + "-" + srcRs.getString("gu_name"));
|
|
741
|
boolean success = equals("Distribution taxonID ", "tu_id: " + String.valueOf(srcRs.getInt("tuId")), destRs.getString("IdInSource"), id);
|
|
742
|
success &= equals("Distribution gazetteer_id ", srcRs.getString("gazetteer_id"), destRs.getString("AreaERMSGazetteerId"), id);
|
|
743
|
success &= equals("Distribution area name ", srcRs.getString("gu_name"), destRs.getString("AreaName"), id);
|
|
744
|
success &= equals("Distribution area name cache", srcRs.getString("gu_name"), destRs.getString("AreaNameCache"), id);
|
|
745
|
success &= equals("Distribution OccurrenceStatusFk", 1, destRs.getInt("OccurrenceStatusFk"), id);
|
|
746
|
success &= equals("Distribution OccurrenceStatusCache", "Present", destRs.getString("OccurrenceStatusCache"), id);
|
|
747
|
//TODO see comments
|
|
748
|
success &= isNull("SourceFk", destRs, id); //sources should be moved to extra table only, check with script and PESI 2014 (=> has values for ERMS)
|
|
749
|
success &= isNull("SourceCache", destRs, id); //sources should be moved to extra table, check with script and PESI 2014 (=> has values for ERMS)
|
|
750
|
success &= equals("Distribution notes ", srcRs.getString("note"), destRs.getString("Notes"), id);
|
|
751
|
success &= isNull("SpeciesExpertGUID", destRs, id); //SpeciesExpertGUID does not exist in ERMS
|
|
752
|
//SpeciesExpertName,LastAction,LastActionDate handled in separate method
|
|
753
|
return success;
|
|
754
|
}
|
|
755
|
|
|
756
|
private boolean testSingleCommonNames(int n) throws SQLException {
|
|
757
|
boolean success = true;
|
|
758
|
ResultSet srcRs = source.getResultSet("SELECT v.*, ISNULL([639_3],[639_2]) iso, l.LanName, tu.id tuId "
|
|
759
|
+ " FROM vernaculars v LEFT JOIN tu ON v.tu_id = tu.id LEFT JOIN languages l ON l.LanID = v.lan_id "
|
|
760
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), ISNULL([639_3],[639_2]), v.vername, v.id ");
|
|
761
|
ResultSet destRs = destination.getResultSet("SELECT cn.*, t.IdInSource, l.ISO639_2, l.ISO639_3 "
|
|
762
|
+ " FROM CommonName cn INNER JOIN Taxon t ON t.TaxonId = cn.TaxonFk LEFT JOIN Language l ON l.LanguageId = cn.LanguageFk "
|
|
763
|
+ " WHERE t." + origErms
|
|
764
|
+ " ORDER BY t.IdInSource, ISNULL("+preferredISO639+", "+alternativeISO639+"), cn.CommonName, cn.LastActionDate "); //sorting also lastActionDate results in a minimum of exact duplicate problems
|
|
765
|
ResultSet srcRsLastAction = source.getResultSet(""
|
|
766
|
+ " SELECT v.id, s.sessiondate, a.action_name, s.ExpertName "
|
|
767
|
+ " FROM vernaculars v "
|
|
768
|
+ " INNER JOIN tu ON tu.id = v.tu_id "
|
|
769
|
+ " LEFT JOIN languages l ON l.LanID = v.lan_id"
|
|
770
|
+ " LEFT JOIN vernaculars_sessions MN ON v.id = MN.vernacular_id "
|
|
771
|
+ " LEFT JOIN actions a ON a.id = MN.action_id "
|
|
772
|
+ " LEFT JOIN sessions s ON s.id = MN.session_id "
|
|
773
|
+ " ORDER BY CAST(tu.id as nvarchar(20)), ISNULL([639_3],[639_2]), v.vername, v.id, s.sessiondate DESC, a.id DESC ");
|
|
774
|
int count = 0;
|
|
775
|
while (srcRs.next() && destRs.next()){
|
|
776
|
success &= testSingleCommonName(srcRs, destRs);
|
|
777
|
success &= testLastAction(srcRsLastAction, destRs, String.valueOf(srcRs.getInt("id")), "CommonName");
|
|
778
|
count++;
|
|
779
|
}
|
|
780
|
success &= equals("Common name count differs", n, count, "-1");
|
|
781
|
return success;
|
|
782
|
}
|
|
783
|
|
|
784
|
boolean prefer639_3 = true;
|
|
785
|
String preferredISO639 = prefer639_3? "ISO639_3":"ISO639_2";
|
|
786
|
String alternativeISO639 = prefer639_3? "ISO639_2":"ISO639_3";
|
|
787
|
|
|
788
|
private boolean testSingleCommonName(ResultSet srcRs, ResultSet destRs) throws SQLException {
|
|
789
|
String id = String.valueOf(srcRs.getInt("tuId") + "-" + srcRs.getString("lan_id"));
|
|
790
|
boolean success = equals("Common name taxonID ", "tu_id: " + String.valueOf(srcRs.getInt("tuId")), destRs.getString("IdInSource"), id);
|
|
791
|
success &= equals("CommonName name ", srcRs.getString("vername"), destRs.getString("CommonName"), id);
|
|
792
|
success &= equals("Common name languageFk ", srcRs.getString("iso"), getLanguageIso(destRs), id);
|
|
793
|
success = equals("CommonName LanguageCache ", normalizeLang(srcRs.getString("LanName")), destRs.getString("LanguageCache"), id);
|
|
794
|
//TODO needed? success = equals("CommonName language code ", srcRs.getString("lan_id"), destRs.getString("LanguageFk"), id);
|
|
795
|
success &= isNull("Region", destRs, id); //region does not seem to exist in ERMS
|
|
796
|
//TODO see comments
|
|
797
|
// success &= isNull("SourceFk", destRs); //sources should be moved to extra table, check with PESI 2014
|
|
798
|
// success &= isNull("SourceNameCache", destRs); //sources should be moved to extra table, check with PESI 2014
|
|
799
|
success &= isNull("SpeciesExpertGUID", destRs, id); //SpeciesExpertGUID does not exist in ERMS
|
|
800
|
//SpeciesExpertName,LastAction,LastActionDate handled in separate method
|
|
801
|
//complete
|
|
802
|
return success;
|
|
803
|
}
|
|
804
|
|
|
805
|
private String normalizeLang(String string) {
|
|
806
|
if ("Spanish".equals(string)){
|
|
807
|
return "Spanish, Castillian";
|
|
808
|
}else if ("Modern Greek (1453-)".equals(string)){
|
|
809
|
return "Greek";
|
|
810
|
}else if ("Malay (individual language)".equals(string)){
|
|
811
|
return "Malay";
|
|
812
|
}else if ("Swahili (individual language)".equals(string)){
|
|
813
|
return "Swahili";
|
|
814
|
}
|
|
815
|
|
|
816
|
return string;
|
|
817
|
}
|
|
818
|
|
|
819
|
private String getLanguageIso(ResultSet destRs) throws SQLException {
|
|
820
|
String result = destRs.getString(preferredISO639);
|
|
821
|
if (result == null){
|
|
822
|
result = destRs.getString(alternativeISO639);
|
|
823
|
}
|
|
824
|
return result;
|
|
825
|
}
|
|
826
|
|
|
827
|
private boolean testSingleReferences() throws SQLException {
|
|
828
|
boolean success = true;
|
|
829
|
ResultSet srcRS = source.getResultSet("SELECT s.* FROM sources s ORDER BY s.id ");
|
|
830
|
ResultSet destRS = destination.getResultSet("SELECT s.* FROM Source s "
|
|
831
|
+ " WHERE s." + origErms
|
|
832
|
+ " ORDER BY s.RefIdInSource "); // +1 for the source reference "erms" but this has no OriginalDB
|
|
833
|
while (srcRS.next() && destRS.next()){
|
|
834
|
success &= testSingleReference(srcRS, destRS);
|
|
835
|
}
|
|
836
|
return success;
|
|
837
|
}
|
|
838
|
|
|
839
|
private boolean testSingleReference(ResultSet srcRS, ResultSet destRS) throws SQLException {
|
|
840
|
String id = String.valueOf(srcRS.getInt("id"));
|
|
841
|
boolean success = equals("Reference ID ", srcRS.getInt("id"), destRS.getInt("RefIdInSource"), id);
|
|
842
|
success &= equals("Reference IMIS_id ", srcRS.getString("imis_id"), destRS.getString("IMIS_Id"), id);
|
|
843
|
success &= equals("Reference SourceCategoryFk ", convertSourceTypeFk(srcRS.getString("source_type")), destRS.getInt("SourceCategoryFk"), id);
|
|
844
|
success &= equals("Reference SourceCategoryCache ", convertSourceTypeCache(srcRS.getString("source_type")), destRS.getString("SourceCategoryCache"), id);
|
|
845
|
success &= equals("Reference name ", srcRS.getString("source_name"), destRS.getString("Name"), id);
|
|
846
|
success &= equals("Reference abstract ", srcRS.getString("source_abstract"), destRS.getString("Abstract"), id);
|
|
847
|
success &= equals("Reference title ", srcRS.getString("source_title"), destRS.getString("Title"), id);
|
|
848
|
success &= equals("Reference author string ", srcRS.getString("source_author"), destRS.getString("AuthorString"), id);
|
|
849
|
success &= equals("Reference year ", normalizeYear(srcRS.getString("source_year")), destRS.getString("RefYear"), id);
|
|
850
|
success &= isNull("NomRefCache", destRS, id); //for ERMS no other value was found in 2014 value
|
|
851
|
success &= equals("Reference link ", srcRS.getString("source_link"), destRS.getString("Link"), id);
|
|
852
|
success &= equals("Reference note ", srcRS.getString("source_note"), destRS.getString("Notes"), id);
|
|
853
|
//complete
|
|
854
|
return success;
|
|
855
|
}
|
|
856
|
|
|
857
|
private Integer convertSourceTypeFk(String sourceType) {
|
|
858
|
if (sourceType == null){
|
|
859
|
return null;
|
|
860
|
}else if ("d".equals(sourceType)){
|
|
861
|
return 4;
|
|
862
|
}else if ("e".equals(sourceType)){
|
|
863
|
return 5;
|
|
864
|
}else if ("p".equals(sourceType)){
|
|
865
|
return 11;
|
|
866
|
}
|
|
867
|
return null;
|
|
868
|
}
|
|
869
|
private String convertSourceTypeCache(String sourceType) {
|
|
870
|
if (sourceType == null){
|
|
871
|
return null;
|
|
872
|
}else if ("d".equals(sourceType)){
|
|
873
|
return "database";
|
|
874
|
}else if ("e".equals(sourceType)){
|
|
875
|
return "informal reference";
|
|
876
|
}else if ("p".equals(sourceType)){
|
|
877
|
return "publication";
|
|
878
|
}
|
|
879
|
return null;
|
|
880
|
}
|
|
881
|
|
|
882
|
private boolean testReferenceCount() {
|
|
883
|
int countSrc = source.getUniqueInteger("SELECT count(*) FROM sources ");
|
|
884
|
int countDest = destination.getUniqueInteger("SELECT count(*) FROM Source s WHERE s."+ origErms); // +1 for the source reference "erms" but this has no OriginalDB
|
|
885
|
boolean success = equals("Reference count ", countSrc, countDest, "-1");
|
|
886
|
return success;
|
|
887
|
}
|
|
888
|
|
|
889
|
//NOTE: there could be better parsing of source_year during import, this may also need better normalizing in the database
|
|
890
|
private String normalizeYear(String yearStr) {
|
|
891
|
if (StringUtils.isBlank(yearStr)){
|
|
892
|
return yearStr;
|
|
893
|
}
|
|
894
|
yearStr = yearStr.trim();
|
|
895
|
if (yearStr.matches("\\d{4}-\\d{2}")){
|
|
896
|
yearStr = yearStr.substring(0, 5)+yearStr.substring(0, 2)+yearStr.substring(5);
|
|
897
|
}
|
|
898
|
if (yearStr.equals("20 Mar 1891")){
|
|
899
|
yearStr = "20.3.1891";
|
|
900
|
}
|
|
901
|
if (yearStr.equals("July 1900")){
|
|
902
|
yearStr = "7.1900";
|
|
903
|
}
|
|
904
|
return yearStr;
|
|
905
|
}
|
|
906
|
|
|
907
|
private boolean isNull(String attrName, ResultSet destRS, String id) throws SQLException {
|
|
908
|
Object value = destRS.getObject(attrName);
|
|
909
|
if (value != null){
|
|
910
|
String message = attrName + " was expected to be null but was: " + value.toString() + "; id = " + id;
|
|
911
|
logger.warn(message);
|
|
912
|
return false;
|
|
913
|
}else{
|
|
914
|
logger.info(attrName + " was null as expected; id = " + id);
|
|
915
|
return true;
|
|
916
|
}
|
|
917
|
}
|
|
918
|
|
|
919
|
private boolean equals(String messageStart, Timestamp srcDate, Timestamp destDate, String id) {
|
|
920
|
if (!CdmUtils.nullSafeEqual(srcDate, destDate)){
|
|
921
|
String message = id + ": " + messageStart + " must be equal, but was not.\n Source: "+ srcDate + "; Destination: " + destDate;
|
|
922
|
logger.warn(message);
|
|
923
|
return false;
|
|
924
|
}else{
|
|
925
|
logger.info(messageStart + " were equal: " + srcDate);
|
|
926
|
return true;
|
|
927
|
}
|
|
928
|
}
|
|
929
|
|
|
930
|
private boolean equals(String messageStart, Integer nSrc, Integer nDest, String id) {
|
|
931
|
String strId = id.equals("-1")? "": (id+ ": ");
|
|
932
|
if (!CdmUtils.nullSafeEqual(nSrc,nDest)){
|
|
933
|
String message = strId+ messageStart + " must be equal, but was not.\n Source: "+ nSrc + "; Destination: " + nDest;
|
|
934
|
logger.warn(message);
|
|
935
|
return false;
|
|
936
|
}else{
|
|
937
|
logger.info(strId + messageStart + " were equal: " + nSrc);
|
|
938
|
return true;
|
|
939
|
}
|
|
940
|
}
|
|
941
|
|
|
942
|
private boolean equals(String messageStart, String strSrc, String strDest, String id) {
|
|
943
|
if (StringUtils.isBlank(strSrc)){
|
|
944
|
strSrc = null;
|
|
945
|
}else{
|
|
946
|
strSrc = strSrc.trim();
|
|
947
|
}
|
|
948
|
//we do not trim strDest here because this should be done during import already. If not it should be shown here
|
|
949
|
if (!CdmUtils.nullSafeEqual(strSrc, strDest)){
|
|
950
|
int index = CdmUtils.diffIndex(strSrc, strDest);
|
|
951
|
String message = id+ ": " + messageStart + " must be equal, but was not at "+index+".\n Source: "+ strSrc + "\n Destination: " + strDest;
|
|
952
|
logger.warn(message);
|
|
953
|
return false;
|
|
954
|
}else{
|
|
955
|
logger.info(id+ ": " + messageStart + " were equal: " + strSrc);
|
|
956
|
return true;
|
|
957
|
}
|
|
958
|
}
|
|
959
|
|
|
960
|
protected Integer nullSafeInt(ResultSet rs, String columnName) throws SQLException {
|
|
961
|
Object intObject = rs.getObject(columnName);
|
|
962
|
if (intObject == null){
|
|
963
|
return null;
|
|
964
|
}else{
|
|
965
|
return Integer.valueOf(intObject.toString());
|
|
966
|
}
|
|
967
|
}
|
|
968
|
|
|
969
|
//** ************* MAIN ********************************************/
|
|
970
|
|
|
971
|
|
|
972
|
|
|
973
|
public static void main(String[] args){
|
|
974
|
PesiErmsValidator validator = new PesiErmsValidator();
|
|
975
|
validator.invoke(defaultSource, defaultDestination);
|
|
976
|
System.exit(0);
|
|
977
|
}
|
|
978
|
}
|