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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.vibrant;
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import java.lang.reflect.Method;
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import java.sql.ResultSet;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
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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.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* TODO add the following to a wiki page:
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* HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen
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* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
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*
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*
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* @author a.mueller
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*
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*/
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public class IopiActivator {
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private static final Logger logger = Logger.getLogger(IopiActivator.class);
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//database validation status (create, update, validate ...)
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static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
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static final Source berlinModelSource = BerlinModelSources.iopi();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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static final ICdmDataSource cdmDestination = cdm_test_local_iopi();
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static final boolean useSingleClassification = true;
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static final Integer sourceSecId = 1892; //7000000;
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static final UUID classificationUuid = null; //UUID.fromString("aa3fbaeb-f5dc-4e75-8d60-c8f93beb7ba6");
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static final UUID sourceRefUuid = UUID.fromString("df68c748-3c64-4b96-9a47-db51fb9d387e");
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// set to zero for unlimited nameFacts
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static final int maximumNumberOfNameFacts = 0;
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static final int partitionSize = 1500;
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//check - import
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static final CHECK check = CHECK.CHECK_AND_IMPORT;
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//editor - import
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
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//NomenclaturalCode
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static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
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//ignore null
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static final boolean ignoreNull = true;
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static boolean useClassification = true;
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//filter
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static String taxonTable = "v_cdm_exp_taxaAll";
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static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
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static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " +
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" FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";
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static String nameIdTable = " v_cdm_exp_namesAll ";
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static String referenceIdTable = " v_cdm_exp_refAll ";
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static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";
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static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";
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static String authorFilter = null; // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) ";
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//not used
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static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
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static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
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// **************** ALL *********************
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//authors
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static final boolean doAuthors = true;
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//references
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
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//names
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static final boolean doTaxonNames = true;
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static final boolean doRelNames = true;
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static final boolean doNameStatus = true;
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//taxa
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static final boolean doTaxa = true;
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static final boolean doRelTaxa = true;
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static final boolean doFacts = true;
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//etc.
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// **************** SELECTED *********************
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// static final boolean doUser = true;
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// //authors
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// static final boolean doAuthors = false;
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// //references
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// static final DO_REFERENCES doReferences = DO_REFERENCES.NONE;
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// //names
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// static final boolean doTaxonNames = false;
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// static final boolean doRelNames = false;
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// static final boolean doNameStatus = false;
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// static final boolean doTypes = false;
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// static final boolean doNameFacts = false;
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//
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// //taxa
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// static final boolean doTaxa = false;
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// static final boolean doRelTaxa = false;
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// static final boolean doFacts = false;
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//
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// //etc.
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// static final boolean doMarker = false;
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//******** ALWAYS IGNORE *****************************
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static final boolean doUser = false;
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static final boolean doOccurences = false;
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static final boolean doCommonNames = false;
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static final boolean doTypes = false;
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static final boolean doNameFacts = false;
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static final boolean doMarker = false;
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public void importIopi (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
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System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
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//make BerlinModel Source
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BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination);
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config.setClassificationUuid(classificationUuid);
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config.setSourceSecId(sourceSecId);
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config.setNomenclaturalCode(nomenclaturalCode);
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try {
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Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);
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config.setMakeUrlForTaxon(makeUrlMethod);
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} catch (Exception e) {
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e.printStackTrace();
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return;
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}
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config.setIgnoreNull(ignoreNull);
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config.setDoAuthors(doAuthors);
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config.setDoReferences(doReferences);
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config.setDoTaxonNames(doTaxonNames);
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config.setDoRelNames(doRelNames);
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config.setDoNameStatus(doNameStatus);
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config.setDoTypes(doTypes);
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config.setDoNameFacts(doNameFacts);
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config.setUseClassification(useClassification);
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config.setSourceRefUuid(sourceRefUuid);
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config.setDoTaxa(doTaxa);
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config.setDoRelTaxa(doRelTaxa);
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config.setDoFacts(doFacts);
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config.setDoOccurrence(doOccurences);
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config.setDoCommonNames(doCommonNames);
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config.setDoMarker(doMarker);
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config.setDoUser(doUser);
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config.setEditor(editor);
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config.setDbSchemaValidation(hbm2dll);
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// maximum number of name facts to import
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config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
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config.setUseSingleClassification(useSingleClassification);
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config.setCheck(check);
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config.setEditor(editor);
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config.setRecordsPerTransaction(partitionSize);
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// filter
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config.setTaxonTable(taxonTable);
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config.setClassificationQuery(classificationQuery);
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config.setRelTaxaIdQuery(relPTaxonIdQuery);
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config.setNameIdTable(nameIdTable);
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config.setReferenceIdTable(referenceIdTable);
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config.setAuthorTeamFilter(authorTeamFilter);
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config.setAuthorFilter(authorFilter);
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config.setFactFilter(factFilter);
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config.setCommonNameFilter(commonNameFilter);
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config.setOccurrenceFilter(occurrenceFilter);
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config.setOccurrenceSourceFilter(occurrenceSourceFilter);
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config.setUseSingleClassification(useSingleClassification);
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// invoke import
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CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();
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bmImport.invoke(config);
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System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
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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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IopiActivator importActivator = new IopiActivator();
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Source source = berlinModelSource;
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ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
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importActivator.importIopi(source, cdmRepository, hbm2dll);
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}
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public static ICdmDataSource cdm_test_local_iopi(){
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
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String cdmServer = "127.0.0.1";
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String cdmDB = "iopi";
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String cdmUserName = "root";
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return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
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}
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//for FAUNA Europaea (http://rbg-web2.rbge.org.uk/FE/fe.html)
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private static final String URLbase = "http://rbg-web2.rbge.org.uk/cgi-bin/nph-readbtree.pl/feout?FAMILY_XREF=%s&GENUS_XREF=%s&SPECIES_XREF=%s&TAXON_NAME_XREF=%s&RANK=%s";
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public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){
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Method result = null;
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ExtensionType urlExtensionType = ExtensionType.URL();
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String family = "";
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String genus = "";
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String species = "";
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String taxonName = "";
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String rankStr = "";
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NonViralName<?> name = CdmBase.deproxy(taxon.getName(), NonViralName.class);
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Rank rank = name.getRank();
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rankStr = transformFeRanks(rank);
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if (rank.equals(Rank.FAMILY())){
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family = name.getGenusOrUninomial();
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taxonName = name.getGenusOrUninomial();
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}else if (rank.isHigher(Rank.GENUS())){
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taxonName = name.getGenusOrUninomial();
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}else if (rank.isGenus()){
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genus = name.getGenusOrUninomial();
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rankStr = "genus";
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}else if (rank.isInfraGeneric()){
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genus = name.getGenusOrUninomial();
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taxonName = name.getInfraGenericEpithet();
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}else if (rank.isSpecies()){
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genus = name.getGenusOrUninomial();
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species = name.getSpecificEpithet();
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rankStr = "species";
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}else if (rank.isInfraSpecific()){
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genus = name.getGenusOrUninomial();
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species = name.getSpecificEpithet();
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taxonName = name.getInfraSpecificEpithet();
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}
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String url = String.format(URLbase ,family, genus, species, taxonName, rankStr);
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taxon.addExtension(url, urlExtensionType);
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return result;
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}
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private static String transformFeRanks(Rank rank){
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if (rank.equals(Rank.SPECIESAGGREGATE())){ return "agg.";
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}else if (rank.equals(Rank.CLASS())){ return "Class";
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}else if (rank.equals(Rank.DIVISION())){ return "Division";
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}else if (rank.equals(Rank.FAMILY())){ return "family";
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}else if (rank.equals(Rank.FORM())){ return "forma";
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}else if (rank.equals(Rank.GENUS())){ return "genus";
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}else if (rank.equals(Rank.GREX())){ return "grex";
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}else if (rank.equals(Rank.SPECIESGROUP())){ return "group";
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}else if (rank.equals(Rank.ORDER())){ return "Order";
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// }else if (rank.equals(Rank.PROL())){ return "proles";
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//-- }else if (rank.equals(Rank.RACE())){ return "race";
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}else if (rank.equals(Rank.SECTION_BOTANY())){ return "Sect.";
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}else if (rank.equals(Rank.SERIES())){ return "Ser.";
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}else if (rank.equals(Rank.SPECIES())){ return "species";
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}else if (rank.equals(Rank.SUBCLASS())){ return "Subclass";
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}else if (rank.equals(Rank.SUBDIVISION())){ return "Subdivision";
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}else if (rank.equals(Rank.SUBFORM())){ return "Subf.";
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}else if (rank.equals(Rank.SUBGENUS())){ return "Subgen.";
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}else if (rank.equals(Rank.SUBORDER())){ return "Suborder";
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}else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return "Subsect.";
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}else if (rank.equals(Rank.SUBSERIES())){ return "Subser.";
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}else if (rank.equals(Rank.SUBSPECIES())){ return "subsp";
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}else if (rank.equals(Rank.SUBVARIETY())){ return "subvar.";
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}else if (rank.equals(Rank.SUPERORDER())){ return "Superorder";
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}else if (rank.equals(Rank.TRIBE())){ return "Tribe";
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}else if (rank.equals(Rank.VARIETY())){ return "var.";
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}else{
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logger.debug("Rank not found: " + rank.getTitleCache());
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return "";
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}
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}
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}
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