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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.pesi;
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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.api.application.ICdmApplicationConfiguration;
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import eu.etaxonomy.cdm.app.common.BerlinModelSources;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.app.common.TreeCreator;
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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.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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 EuroMedActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(EuroMedActivator.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.euroMed();
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static final Source berlinModelSource = BerlinModelSources.PESI3_euroMed();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euroMed();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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static final boolean includePesiExport = false;
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static final int sourceSecId = 7000000; //500000
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static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
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static final boolean useSingleClassification = true;
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static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
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static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
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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 = 5000;
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//check - import
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
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//editor - import
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static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
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//NomeclaturalCode
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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 final boolean switchSpeciesGroup = true;
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static boolean useClassification = true;
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static boolean isSplitTdwgCodes = false;
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private boolean removeHttpMapsAnchor = true;
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static final String infrGenericRankAbbrev = "[unranked]";
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static final String infrSpecificRankAbbrev = "[unranked]";
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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 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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static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
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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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// **************** ALL *********************
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static final boolean doUser = true;
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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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static final boolean doTypes = false; //serious types do not exist in E+M
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static final boolean doNameFacts = 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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static final boolean doOccurences = true;
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static final boolean doCommonNames = false; //FIXME currently common names throw errors and make later imports not work
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//etc.
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static final boolean doMarker = true;
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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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// static final boolean doOccurences = false;
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// static final boolean doCommonNames = false;
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//
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// //etc.
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// static final boolean doMarker = false;
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public void importEm2CDM (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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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(PesiTransformer.uuidSourceRefEuroMed);
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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.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
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config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
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config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
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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.setWebMarkerFilter(webMarkerFilter);
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config.setUseSingleClassification(useSingleClassification);
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//TDWG codes
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config.setSplitTdwgCodes(isSplitTdwgCodes);
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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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config.setSwitchSpeciesGroup(switchSpeciesGroup);
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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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if (doFacts && config.getCheck().equals(CHECK.CHECK_AND_IMPORT) || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) ){
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ICdmApplicationConfiguration app = bmImport.getCdmAppController();
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//make feature tree
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FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
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FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());
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tree.getRoot().addChild(imageNode);
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FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());
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tree.getRoot().addChild(distributionNode, 2);
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app.getFeatureTreeService().saveOrUpdate(tree);
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}
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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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EuroMedActivator importActivator = new EuroMedActivator();
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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.importEm2CDM(source, cdmRepository, hbm2dll);
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if (includePesiExport){
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PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();
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exportActivator.doExport(cdmRepository);
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}
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}
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}
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