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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.algaterra;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraTypeImportValidator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelReferenceImport;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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*/
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@Component
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public class AlgaTerraTypeImport extends AlgaTerraSpecimenImportBase {
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private static final Logger logger = Logger.getLogger(AlgaTerraTypeImport.class);
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private static int modCount = 5000;
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private static final String pluralString = "types";
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private static final String dbTableName = "TypeDesignation"; //??
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protected String getLocalityString(){
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return "TypeLocality";
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}
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public AlgaTerraTypeImport(){
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super(dbTableName, pluralString);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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String result = " SELECT TypeDesignationId "
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+ " FROM TypeDesignation "
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+ " ORDER BY NameFk ";
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery =
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" SELECT ts.*, ts.TypeSpecimenId as unitId, td.*, gz.ID as GazetteerId, gz.L2Code, gz.L3Code, gz.L4Code, gz.ISOCountry, gz.Country, ts.WaterBody " +
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" " +
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" FROM TypeSpecimenDesignation tsd "
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+ " LEFT OUTER JOIN TypeSpecimen AS ts ON tsd.TypeSpecimenFk = ts.TypeSpecimenId "
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+ " FULL OUTER JOIN TypeDesignation td ON td.TypeDesignationId = tsd.TypeDesignationFk "
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+ " LEFT OUTER JOIN TDWGGazetteer gz ON ts.TDWGGazetteerFk = gz.ID "
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+ " WHERE (td.TypeDesignationId IN (" + ID_LIST_TOKEN + ") )"
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+ " ORDER BY NameFk "
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;
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
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boolean success = true;
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AlgaTerraImportState state = (AlgaTerraImportState)bmState;
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//TODO check that no duplicate vocabularies will be created, also remove redundant code here
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// and in Specimen importer
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try {
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makeVocabulariesAndFeatures(state);
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} catch (SQLException e1) {
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logger.warn("Exception occurred when trying to create Type specimen vocabularies: " + e1.getMessage());
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e1.printStackTrace();
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}
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Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
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Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
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Map<String, DerivedUnit> ecoFactMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(AlgaTerraSpecimenImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE);
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Map<String, DerivedUnit> typeSpecimenMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE);
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Map<String, Reference> biblioReference = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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try {
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Type designations handled: " + (i-1));}
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int nameId = rs.getInt("nameFk");
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int typeSpecimenId = rs.getInt("TypeSpecimenId");
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int typeDesignationId = rs.getInt("TypeDesignationId");
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Integer typeStatusFk = nullSafeInt(rs, "typeStatusFk");
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Integer ecoFactId = nullSafeInt(rs, "ecoFactFk");
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// String recordBasis = rs.getString("RecordBasis");
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try {
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//source ref
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Reference<?> sourceRef = state.getTransactionalSourceReference();
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//facade
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//FIXME - depends on material category
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// DerivedUnitType type = makeDerivedUnitType(recordBasis);
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DerivedUnitType type = DerivedUnitType.Specimen;
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DerivedUnitFacade facade = getDerivedUnit(state, typeSpecimenId, typeSpecimenMap, type, ecoFactMap, ecoFactId);
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//field observation
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handleSingleSpecimen(rs, facade, state, partitioner);
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handleTypeSpecimenSpecificSpecimen(rs,facade, state);
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state.setCurrentFieldObservationNotNew(false);
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//Designation
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TaxonNameBase<?,?> name = getTaxonName(state, taxonNameMap, nameId);
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SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
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SpecimenTypeDesignationStatus status = getSpecimenTypeDesignationStatusByKey(typeStatusFk);
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designation.setTypeSpecimen(facade.innerDerivedUnit());
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designation.setTypeStatus(status);
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if (name != null){
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name.addTypeDesignation(designation, true); //TODO check if true is correct
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}else{
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logger.warn("Name could not be found for type designation " + typeDesignationId);
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}
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namesToSave.add(name);
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} catch (Exception e) {
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logger.warn("Exception in TypeDesignation: TypeDesignationId " + typeDesignationId + ". " + e.getMessage());
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e.printStackTrace();
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}
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}
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// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
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logger.warn("Names to save: " + namesToSave.size());
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getNameService().save(namesToSave);
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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}
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protected String getDerivedUnitNameSpace(){
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return TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE;
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}
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/**
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* @param state
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* @param taxonNameMap
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* @param nameId
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* @return
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*/
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private TaxonNameBase<?,?> getTaxonName(AlgaTerraImportState state, Map<String, TaxonNameBase> taxonNameMap, int nameId) {
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TaxonNameBase<?,?> result;
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if (state.getConfig().isDoTaxonNames()){
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result = taxonNameMap.get(String.valueOf(nameId));
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}else{
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//for testing
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result = BotanicalName.NewInstance(Rank.SPECIES());
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}
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return result;
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}
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private void handleTypeSpecimenSpecificSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
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//TODO
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//collection
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String barcode = rs.getString("Barcode");
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if (StringUtils.isNotBlank(barcode)){
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facade.setBarcode(barcode);
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}
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}
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/**
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* @param state
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* @param ecoFactId
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* @param derivedUnitMap
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* @param type
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* @param ecoFactId2
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* @param ecoFactMap
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* @return
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*/
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private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int typeSpecimenId, Map<String, DerivedUnit> typeSpecimenMap, DerivedUnitType type, Map<String, DerivedUnit> ecoFactMap, Integer ecoFactId2) {
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//TODO implement ecoFact map - if not all null anymore
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String typeKey = String.valueOf(typeSpecimenId);
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DerivedUnit derivedUnit = typeSpecimenMap.get(typeKey);
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DerivedUnitFacade facade;
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if (derivedUnit == null){
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facade = DerivedUnitFacade.NewInstance(type);
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typeSpecimenMap.put(typeKey, derivedUnit);
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}else{
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try {
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facade = DerivedUnitFacade.NewInstance(derivedUnit);
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} catch (DerivedUnitFacadeNotSupportedException e) {
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logger.error(e.getMessage());
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facade = DerivedUnitFacade.NewInstance(type);
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}
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}
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return facade;
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}
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private DerivedUnitType makeDerivedUnitType(String recordBasis) {
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DerivedUnitType result = null;
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if (StringUtils.isBlank(recordBasis)){
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result = DerivedUnitType.DerivedUnit;
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} else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
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result = DerivedUnitType.Fossil;
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}else if (recordBasis.equalsIgnoreCase("HumanObservation")){
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result = DerivedUnitType.Observation;
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}else if (recordBasis.equalsIgnoreCase("Literature")){
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logger.warn("Literature record basis not yet supported");
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result = DerivedUnitType.DerivedUnit;
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}else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
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result = DerivedUnitType.LivingBeing;
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}else if (recordBasis.equalsIgnoreCase("MachineObservation")){
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logger.warn("MachineObservation record basis not yet supported");
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result = DerivedUnitType.Observation;
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}else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
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result = DerivedUnitType.Specimen;
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}
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return result;
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}
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private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(Integer typeStatusFk) {
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if (typeStatusFk == null){ return null;
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}else if (typeStatusFk == 1) { return SpecimenTypeDesignationStatus.HOLOTYPE();
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}else if (typeStatusFk == 2) { return SpecimenTypeDesignationStatus.LECTOTYPE();
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}else if (typeStatusFk == 3) { return SpecimenTypeDesignationStatus.NEOTYPE();
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}else if (typeStatusFk == 4) { return SpecimenTypeDesignationStatus.EPITYPE();
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}else if (typeStatusFk == 5) { return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
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}else if (typeStatusFk == 6) { return SpecimenTypeDesignationStatus.ISONEOTYPE();
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}else if (typeStatusFk == 7) { return SpecimenTypeDesignationStatus.ISOTYPE();
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}else if (typeStatusFk == 8) { return SpecimenTypeDesignationStatus.PARANEOTYPE();
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}else if (typeStatusFk == 9) { return SpecimenTypeDesignationStatus.PARATYPE();
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}else if (typeStatusFk == 10) { return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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}else if (typeStatusFk == 11) { return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
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}else if (typeStatusFk == 12) { return SpecimenTypeDesignationStatus.SYNTYPE();
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}else if (typeStatusFk == 13) { return SpecimenTypeDesignationStatus.PARALECTOTYPE();
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}else if (typeStatusFk == 14) { return SpecimenTypeDesignationStatus.ISOEPITYPE();
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}else if (typeStatusFk == 21) { return SpecimenTypeDesignationStatus.ICONOTYPE();
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}else if (typeStatusFk == 22) { return SpecimenTypeDesignationStatus.PHOTOTYPE();
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}else if (typeStatusFk == 30) { return SpecimenTypeDesignationStatus.TYPE();
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}else if (typeStatusFk == 38) { return SpecimenTypeDesignationStatus.ISOEPITYPE();
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// }else if (typeStatusFk == 39) { return SpecimenTypeDesignationStatus.;
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}else if (typeStatusFk == 40) { return SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL();
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}else{
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logger.warn("typeStatusFk undefined for " + typeStatusFk);
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return SpecimenTypeDesignationStatus.TYPE();
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace;
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Class cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> nameIdSet = new HashSet<String>();
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Set<String> ecoFieldObservationIdSet = new HashSet<String>();
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Set<String> typeSpecimenIdSet = new HashSet<String>();
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Set<String> termsIdSet = new HashSet<String>();
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Set<String> collectionIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, nameIdSet, "nameFk");
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handleForeignKey(rs, ecoFieldObservationIdSet, "ecoFactFk");
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handleForeignKey(rs, typeSpecimenIdSet, "TypeSpecimenId");
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handleForeignKey(rs, collectionIdSet, "CollectionFk");
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}
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331
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//name map
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nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
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334
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cdmClass = TaxonNameBase.class;
|
|
335
|
idSet = nameIdSet;
|
|
336
|
Map<String, TaxonNameBase> objectMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
337
|
result.put(nameSpace, objectMap);
|
|
338
|
|
|
339
|
//eco fact field observation map
|
|
340
|
nameSpace = AlgaTerraTypeImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE;
|
|
341
|
cdmClass = FieldObservation.class;
|
|
342
|
idSet = ecoFieldObservationIdSet;
|
|
343
|
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
344
|
result.put(nameSpace, fieldObservationMap);
|
|
345
|
|
|
346
|
//type specimen map
|
|
347
|
nameSpace = AlgaTerraTypeImport.TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE;
|
|
348
|
cdmClass = FieldObservation.class;
|
|
349
|
idSet = typeSpecimenIdSet;
|
|
350
|
Map<String, FieldObservation> typeSpecimenMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
351
|
result.put(nameSpace, typeSpecimenMap);
|
|
352
|
|
|
353
|
|
|
354
|
//collections
|
|
355
|
nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION;
|
|
356
|
cdmClass = Collection.class;
|
|
357
|
idSet = collectionIdSet;
|
|
358
|
Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
359
|
result.put(nameSpace, collectionMap);
|
|
360
|
|
|
361
|
//sub-collections
|
|
362
|
nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION;
|
|
363
|
cdmClass = Collection.class;
|
|
364
|
idSet = collectionIdSet;
|
|
365
|
Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
366
|
result.put(nameSpace, subCollectionMap);
|
|
367
|
|
|
368
|
|
|
369
|
//
|
|
370
|
// //terms
|
|
371
|
// nameSpace = AlgaTerraTypeImport.TERMS_NAMESPACE;
|
|
372
|
// cdmClass = FieldObservation.class;
|
|
373
|
// idSet = taxonIdSet;
|
|
374
|
// Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
375
|
// result.put(nameSpace, termMap);
|
|
376
|
|
|
377
|
|
|
378
|
|
|
379
|
|
|
380
|
} catch (SQLException e) {
|
|
381
|
throw new RuntimeException(e);
|
|
382
|
}
|
|
383
|
return result;
|
|
384
|
}
|
|
385
|
|
|
386
|
/* (non-Javadoc)
|
|
387
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
388
|
*/
|
|
389
|
@Override
|
|
390
|
protected boolean doCheck(BerlinModelImportState state){
|
|
391
|
IOValidator<BerlinModelImportState> validator = new AlgaTerraTypeImportValidator();
|
|
392
|
return validator.validate(state);
|
|
393
|
}
|
|
394
|
|
|
395
|
|
|
396
|
/* (non-Javadoc)
|
|
397
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
398
|
*/
|
|
399
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
400
|
return ! state.getConfig().isDoTypes();
|
|
401
|
}
|
|
402
|
|
|
403
|
}
|