Revision 8422c0cd
Added by Andreas Müller almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCommonNameImport.java | ||
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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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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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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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import eu.etaxonomy.cdm.model.common.TimePeriod; |
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import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.location.Country; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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/** |
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* @author a.mueller |
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* @created 20.02.2010 |
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*
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* |
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* OPEN ISSUES: |
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*
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* |
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* ... |
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*/ |
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@Component |
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public class GlobisCommonNameImport extends GlobisImportBase<Taxon> {
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private static final Logger logger = Logger.getLogger(GlobisCommonNameImport.class); |
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private int modCount = 10000; |
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private static final String pluralString = "common names"; |
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private static final String dbTableName = "species_language"; |
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private static final Class<?> cdmTargetClass = Taxon.class; //not needed |
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public GlobisCommonNameImport(){
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super(pluralString, dbTableName, cdmTargetClass); |
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} |
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//dirty but acceptable for globis environment |
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private Map<Integer,Reference> refMap = new HashMap<Integer,Reference>(); |
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@Override |
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protected String getIdQuery() {
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String strRecordQuery =
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" SELECT ID " +
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" FROM " + dbTableName;
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return strRecordQuery;
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String strRecordQuery = |
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" SELECT ID " + |
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" FROM " + dbTableName; |
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return strRecordQuery; |
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} |
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@Override |
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protected String getRecordQuery(GlobisImportConfigurator config) {
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String strRecordQuery =
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" SELECT * " +
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String strRecordQuery = |
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" SELECT * " + |
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" FROM " + getTableName() + " sl " + |
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" WHERE ( sl.ID IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery; |
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} |
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@Override |
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public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
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boolean success = true; |
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Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>(); |
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Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);
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Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_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 common name |
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
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Integer idTaxon = nullSafeInt(rs,"IDCurrentSpec"); |
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try {
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//source ref |
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Reference<?> sourceRef = state.getTransactionalSourceReference();
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Reference sourceRef = state.getTransactionalSourceReference(); |
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//common names |
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Integer id = nullSafeInt(rs,"ID"); |
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String isoLang = rs.getString("ISO");
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String strCommonName = rs.getString("commonname");
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Integer refID = nullSafeInt(rs,"ReferenceID"); |
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String strCountryCode = rs.getString("Code2");
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Taxon taxon = taxonMap.get(String.valueOf(idTaxon)); |
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if (taxon == null){
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logger.warn("No taxon found for taxonId " + idTaxon);
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TaxonDescription taxonDescription = getTaxonDescription(taxon, sourceRef, ! IMAGE_GALLERY, CREATE); |
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CommonTaxonName commonName = CommonTaxonName.NewInstance(strCommonName, language, area); |
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taxonDescription.addElement(commonName); |
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Reference<?> ref = handleReference(state, refID);
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Reference ref = handleReference(state, refID); |
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if (ref == null && refID != null){
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logger.warn("No reference found for common name ID: " + id);
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}else{
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commonName.addSource(OriginalSourceType.Import, String.valueOf(refID), "reference", sourceRef, null); |
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} |
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objectsToSave.add(taxon);
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objectsToSave.add(taxon); |
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} |
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} catch (Exception e) {
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logger.warn("Exception in current_species: IDcurrentspec " + idTaxon + ". " + e.getMessage());
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e.printStackTrace(); |
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}
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} |
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} |
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logger.warn(pluralString + " to save: " + objectsToSave.size()); |
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getTaxonService().save(objectsToSave);
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getTaxonService().save(objectsToSave); |
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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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} |
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} |
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private Map<String,Language> languageMap = new HashMap<String,Language>(); |
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private Language getLanguage(String isoLang) {
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Language result = languageMap.get(isoLang); |
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if (result == null){
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result = getTermService().getLanguageByIso(isoLang); |
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if (result == null){
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logger.warn("No language found for iso code: " + isoLang);
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return result; |
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} |
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private Reference<?> handleReference(GlobisImportState state, Integer refId){
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private Reference handleReference(GlobisImportState state, Integer refId){
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if (refId == null){
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return null; |
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} |
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Reference<?> result = refMap.get(refId);
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Reference result = refMap.get(refId); |
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if (result == null){
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try {
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String sql = "SELECT * FROM [references] WHERE ReferenceID = " + refId; |
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ResultSet rs = state.getConfig().getSource().getResultSet(sql); |
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rs.next(); |
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String authors = rs.getString("Author(s)");
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String title = rs.getString("Title");
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String details = rs.getString("Details");
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}else{
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author = makeSingleAuthor(authors); |
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} |
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result.setAuthorship(author); |
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refMap.put(refId,result); |
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rs.close(); |
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e.printStackTrace(); |
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} |
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} |
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return result; |
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} |
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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> taxonIdSet = new HashSet<String>(); |
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "IDCurrentSpec"); |
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} |
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//taxon map |
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nameSpace = TAXON_NAMESPACE; |
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cdmClass = Taxon.class; |
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Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, objectMap); |
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} catch (SQLException e) {
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throw new RuntimeException(e); |
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} |
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return result; |
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} |
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@Override |
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protected boolean doCheck(GlobisImportState state){
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// IOValidator<GlobisImportState> validator = new GlobisCurrentSpeciesImportValidator(); |
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return true; |
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} |
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@Override |
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protected boolean isIgnore(GlobisImportState state){
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return ! state.getConfig().isDoCommonNames(); |
Also available in: Unified diff
Remove generics from Reference in cdmlib-app #5830