Revision a399b702
Added by U-BGBM\k.luther over 8 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaVernacularNamesImport.java | ||
|---|---|---|
| 14 | 14 |
import java.util.Map.Entry; |
| 15 | 15 |
|
| 16 | 16 |
import org.apache.log4j.Logger; |
| 17 |
import org.springframework.stereotype.Component; |
|
| 17 | 18 |
import org.springframework.transaction.TransactionStatus; |
| 18 | 19 |
|
| 19 | 20 |
import eu.etaxonomy.cdm.io.common.Source; |
| 21 |
import eu.etaxonomy.cdm.jaxb.TDWGNamespacePrefixMapper; |
|
| 20 | 22 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 21 | 23 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 22 | 24 |
import eu.etaxonomy.cdm.model.common.Language; |
| 23 | 25 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
| 26 |
import eu.etaxonomy.cdm.model.common.TermType; |
|
| 24 | 27 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
| 25 | 28 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 26 | 29 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
| ... | ... | |
| 30 | 33 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 31 | 34 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 32 | 35 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 36 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 33 | 37 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 34 | 38 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 35 | 39 |
|
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@Component |
|
| 36 | 41 |
public class FaunaEuropaeaVernacularNamesImport extends FaunaEuropaeaImportBase {
|
| 37 | 42 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaVernacularNamesImport.class); |
| 38 | 43 |
|
| ... | ... | |
| 42 | 47 |
protected void doInvoke(FaunaEuropaeaImportState state) {
|
| 43 | 48 |
int limit = state.getConfig().getLimitSave(); |
| 44 | 49 |
|
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/* Taxon store for retrieving taxa from and saving taxa to CDM */ |
|
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List<TaxonBase> taxonList = null; |
|
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/* UUID store as input for retrieving taxa from CDM */ |
|
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Set<UUID> taxonUuids = null; |
|
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/* Store to hold helper objects */ |
|
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Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null; |
|
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|
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|
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TransactionStatus txStatus = null; |
|
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|
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createSourceMap(state); |
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|
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
|
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Source source = fauEuConfig.getSource(); |
|
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|
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int i = 0; |
|
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|
|
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String selectCount = |
|
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" SELECT count(*) "; |
|
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|
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String selectColumns = |
|
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" SELECT vernacularName.*, Taxon.UUID "; |
|
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|
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String fromClause = |
|
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" FROM vernacularName INNER JOIN " + |
|
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" Taxon ON vernacularname.taxon_UUID = Taxon.UUID "; |
|
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String orderBy = " ORDER BY vernacularName.taxon_UUID"; |
|
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|
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String countQuery = |
|
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selectCount + fromClause; |
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|
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String selectQuery = |
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selectColumns + fromClause + orderBy; |
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if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }
|
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|
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try {
|
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ResultSet rs = source.getResultSet(countQuery); |
|
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rs.next(); |
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int count = rs.getInt(1); |
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|
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rs = source.getResultSet(selectQuery); |
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQuery);
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logger.info("Select Query: " + selectQuery);
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} |
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|
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//int taxonId; |
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|
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while (rs.next()) {
|
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if ((i++ % limit) == 0) {
|
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|
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txStatus = startTransaction(); |
|
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taxonUuids = new HashSet<UUID>(limit); |
|
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fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit); |
|
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|
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if(logger.isInfoEnabled()) {
|
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logger.info("i = " + i + " - Distribution import transaction started");
|
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} |
|
| 50 |
if (state.getConfig().isDoVernacularNames()){
|
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/* Taxon store for retrieving taxa from and saving taxa to CDM */ |
|
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List<TaxonBase> taxonList = null; |
|
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/* UUID store as input for retrieving taxa from CDM */ |
|
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Set<UUID> taxonUuids = null; |
|
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/* Store to hold helper objects */ |
|
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Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null; |
|
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|
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|
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TransactionStatus txStatus = null; |
|
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|
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createSourceMap(state); |
|
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|
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
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Source source = fauEuConfig.getSource(); |
|
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|
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int i = 0; |
|
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|
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String selectCount = |
|
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" SELECT count(*) "; |
|
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|
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String selectColumns = |
|
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" SELECT vernacularNames.*, Taxon.UUID "; |
|
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|
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String fromClause = |
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" FROM vernacularNames INNER JOIN " + |
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" Taxon ON vernacularnames.UUID = Taxon.UUID "; |
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String orderBy = " ORDER BY vernacularNames.UUID"; |
|
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|
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String countQuery = |
|
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selectCount + fromClause; |
|
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|
|
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String selectQuery = |
|
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selectColumns + fromClause + orderBy; |
|
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|
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|
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|
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if(logger.isInfoEnabled()) { logger.info("Start making vernacular names..."); }
|
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|
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try {
|
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ResultSet rs = source.getResultSet(countQuery); |
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rs.next(); |
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int count = rs.getInt(1); |
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|
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rs = source.getResultSet(selectQuery); |
|
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|
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
|
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logger.info("Count Query: " + countQuery);
|
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logger.info("Select Query: " + selectQuery);
|
|
| 108 | 100 |
} |
| 109 |
|
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//taxonId = rs.getInt("dis_tax_id");
|
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String vernameGUID = rs.getString("GUID");
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String vernacularNameString = rs.getString("verName");
|
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int taxonFk = rs.getInt("taxonFK");
|
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int languageFK= rs.getInt("languageFK");
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String languageCache = rs.getString("languageCache");
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String taxonUUID= rs.getString("taxonUUID");
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String verSource = rs.getString("VerSource");
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UUID currentTaxonUuid = null; |
|
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|
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|
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FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName(); |
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fauEuVernacularName.setGuid(vernameGUID); |
|
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fauEuVernacularName.setLanguageCache(languageCache); |
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fauEuVernacularName.setLanguageFk(languageFK); |
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fauEuVernacularName.setVernacularName(vernacularNameString); |
|
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fauEuVernacularName.setSource(verSource); |
|
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|
|
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if (!taxonUuids.contains(currentTaxonUuid)) {
|
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taxonUuids.add(currentTaxonUuid); |
|
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FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon = |
|
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new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid); |
|
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fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon); |
|
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fauEuVernacularNameTaxon = null; |
|
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} else {
|
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if (logger.isTraceEnabled()) {
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logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
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continue; |
|
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|
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//int taxonId; |
|
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|
|
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while (rs.next()) {
|
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if ((i++ % limit) == 0) {
|
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|
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txStatus = startTransaction(); |
|
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taxonUuids = new HashSet<UUID>(limit); |
|
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fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit); |
|
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|
|
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if(logger.isInfoEnabled()) {
|
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logger.info("i = " + i + " - vernacular names import transaction started");
|
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} |
|
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} |
|
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|
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//taxonId = rs.getInt("dis_tax_id");
|
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String vernameGUID = rs.getString("GUID");
|
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String vernacularNameString = rs.getString("verName");
|
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//int taxonFk = rs.getInt("taxonFK");
|
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int languageFK= rs.getInt("languageFK");
|
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String languageCache = rs.getString("languageCache");
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String taxonUUID= rs.getString("UUID");
|
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String verSource = rs.getString("VerSource");
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UUID currentTaxonUuid = null; |
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|
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| 126 |
|
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FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName(); |
|
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fauEuVernacularName.setGuid(vernameGUID); |
|
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fauEuVernacularName.setLanguageCache(languageCache); |
|
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fauEuVernacularName.setLanguageFk(languageFK); |
|
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fauEuVernacularName.setVernacularName(vernacularNameString); |
|
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fauEuVernacularName.setSource(verSource); |
|
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fauEuVernacularName.setTaxonUuid(UUID.fromString(taxonUUID)); |
|
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currentTaxonUuid =UUID.fromString(taxonUUID); |
|
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if (!taxonUuids.contains(currentTaxonUuid)) {
|
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taxonUuids.add(currentTaxonUuid); |
|
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FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon = |
|
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new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid); |
|
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fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon); |
|
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fauEuVernacularNameTaxon = null; |
|
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} else {
|
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if (logger.isTraceEnabled()) {
|
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logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
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continue; |
|
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} |
|
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} |
|
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|
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fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName); |
|
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|
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if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
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|
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try {
|
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus); |
|
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taxonUuids = null; |
|
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taxonList = null; |
|
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fauEuVernacularNamesMap = null; |
|
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|
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} catch (Exception e) {
|
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logger.error("Commit of taxa and distributions failed" + e.getMessage());
|
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e.printStackTrace(); |
|
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} |
|
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|
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if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
|
|
| 138 | 164 |
} |
| 165 |
|
|
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|
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| 139 | 167 |
} |
| 140 |
|
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fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName); |
|
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|
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if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
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| 144 |
|
|
| 168 |
if (taxonUuids != null){
|
|
| 145 | 169 |
try {
|
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
|
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus); |
|
| 147 | 171 |
taxonUuids = null; |
| 148 | 172 |
taxonList = null; |
| 149 | 173 |
fauEuVernacularNamesMap = null; |
| 150 |
|
|
| 151 | 174 |
} catch (Exception e) {
|
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logger.error("Commit of taxa and distributions failed" + e.getMessage());
|
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logger.error("Commit of taxa and vernacular names failed");
|
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logger.error(e.getMessage()); |
|
| 153 | 177 |
e.printStackTrace(); |
| 154 | 178 |
} |
| 155 |
|
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if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
|
|
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} |
|
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|
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| 159 |
|
|
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} |
|
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if (taxonUuids != null){
|
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try {
|
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commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus); |
|
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taxonUuids = null; |
|
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taxonList = null; |
|
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fauEuVernacularNamesMap = null; |
|
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} catch (Exception e) {
|
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| 168 |
logger.error("Commit of taxa and distributions failed");
|
|
| 169 |
logger.error(e.getMessage()); |
|
| 170 |
e.printStackTrace(); |
|
| 171 | 179 |
} |
| 180 |
rs = null; |
|
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} catch (SQLException e) {
|
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| 182 |
logger.error("SQLException:" + e);
|
|
| 183 |
state.setUnsuccessfull(); |
|
| 172 | 184 |
} |
| 173 |
rs = null; |
|
| 174 |
} catch (SQLException e) {
|
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| 175 |
logger.error("SQLException:" + e);
|
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| 176 |
state.setUnsuccessfull();
|
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| 185 |
|
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| 186 |
if(logger.isInfoEnabled()) { logger.info("End making vernacular names..."); }
|
|
| 187 |
|
|
| 188 |
return;
|
|
| 177 | 189 |
} |
| 178 | 190 |
|
| 179 |
if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
|
|
| 180 |
|
|
| 181 |
return; |
|
| 182 |
|
|
| 183 | 191 |
} |
| 184 | 192 |
|
| 185 | 193 |
@Override |
| ... | ... | |
| 198 | 206 |
Set<UUID> taxonUuids, |
| 199 | 207 |
Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap, |
| 200 | 208 |
TransactionStatus txStatus) throws Exception {
|
| 201 |
List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
|
|
| 209 |
List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state); |
|
| 202 | 210 |
|
| 203 |
getTaxonService().save(taxonList); |
|
| 211 |
getTaxonService().saveOrUpdate(taxonList);
|
|
| 204 | 212 |
taxonList = null; |
| 205 | 213 |
taxonUuids = null; |
| 206 | 214 |
fauEuTaxonMap = null; |
| ... | ... | |
| 224 | 232 |
if (taxonBase instanceof Taxon) {
|
| 225 | 233 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
| 226 | 234 |
} else {
|
| 235 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 236 |
if (syn.getAcceptedTaxa().size()>0){
|
|
| 237 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
|
| 238 |
} |
|
| 227 | 239 |
logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
|
| 228 |
+ taxonBase.getClass().getSimpleName()); |
|
| 240 |
+ taxonBase.getClass().getSimpleName() + " using accepted Taxon for vernacular name");
|
|
| 229 | 241 |
continue; |
| 230 | 242 |
} |
| 231 | 243 |
|
| 232 | 244 |
|
| 233 | 245 |
Set<TaxonDescription> descriptionSet = taxon.getDescriptions(); |
| 234 |
if (descriptionSet.size() > 0) {
|
|
| 235 |
taxonDescription = descriptionSet.iterator().next(); |
|
| 236 |
} else {
|
|
| 237 |
taxonDescription = TaxonDescription.NewInstance(); |
|
| 238 |
taxon.addDescription(taxonDescription); |
|
| 239 |
} |
|
| 246 |
taxonDescription = TaxonDescription.NewInstance(); |
|
| 247 |
taxon.addDescription(taxonDescription); |
|
| 248 |
|
|
| 240 | 249 |
|
| 241 | 250 |
taxonUuid = taxonBase.getUuid(); |
| 242 | 251 |
fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid); |
| ... | ... | |
| 244 | 253 |
for (FaunaEuropaeaVernacularName fauEuHelperVernacularName: fauEuHelperTaxon.getVernacularNames()) {
|
| 245 | 254 |
|
| 246 | 255 |
verName = null; |
| 256 |
|
|
| 257 |
/* |
|
| 258 |
* UUID uuid = state.getTransformer().getLanguageUuid(languageKey); |
|
| 259 |
result = (Language)getTermService().find(uuid); |
|
| 260 |
} |
|
| 261 |
if (result == null){
|
|
| 262 |
result = state.getTransformer().getLanguageByKey(languageKey); |
|
| 263 |
if (result == null){
|
|
| 264 |
UUID uuidLanguage; |
|
| 265 |
uuidLanguage = state.getTransformer().getLanguageUuid(languageKey); |
|
| 266 |
if (uuidLanguage == null){
|
|
| 267 |
logger.warn("Language not defined: " + languageKey) ;
|
|
| 268 |
} |
|
| 269 |
result = getLanguage(state, uuidLanguage, languageKey, languageKey, null); |
|
| 270 |
if (result == null){
|
|
| 271 |
logger.warn("Language not defined: " + languageKey) ;
|
|
| 272 |
} |
|
| 273 |
}else if (result.getId() == 0){
|
|
| 274 |
// UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de");
|
|
| 275 |
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
| 276 |
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result); |
|
| 277 |
// TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc); |
|
| 278 |
voc.addTerm(result); |
|
| 279 |
getTermService().saveOrUpdate(result); |
|
| 280 |
state.putLanguage(result); |
|
| 281 |
} |
|
| 282 |
* |
|
| 283 |
*/ |
|
| 247 | 284 |
Language lang = FaunaEuropaeaTransformer.langFK2Language(fauEuHelperVernacularName.getLanguageFk()); |
| 285 |
if (lang == null && fauEuHelperVernacularName.getLanguageFk() == 83){
|
|
| 286 |
lang = Language.ENGLISH(); |
|
| 287 |
fauEuHelperVernacularName.setArea("USA");
|
|
| 288 |
} |
|
| 289 |
|
|
| 290 |
if (lang == null){
|
|
| 291 |
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
| 292 |
logger.info("languageFk = " + fauEuHelperVernacularName.getLanguageFk());
|
|
| 293 |
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang); |
|
| 294 |
lang = Language.NewInstance("Dummy", "", "");
|
|
| 295 |
voc.addTerm(lang); |
|
| 296 |
lang =(Language)getTermService().save(lang); |
|
| 297 |
FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang); |
|
| 298 |
} |
|
| 299 |
// if (lang.getId() == 0){
|
|
| 300 |
// UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
| 301 |
// TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang); |
|
| 302 |
// voc.addTerm(lang); |
|
| 303 |
// lang =(Language)getTermService().save(lang); |
|
| 304 |
// //FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang); |
|
| 305 |
// } |
|
| 306 |
|
|
| 248 | 307 |
verName = CommonTaxonName.NewInstance(fauEuHelperVernacularName.getVernacularName(), lang); |
| 308 |
if (fauEuHelperVernacularName.getArea()!= null && fauEuHelperVernacularName.getArea().equals("USA")){
|
|
| 309 |
verName.setArea(NamedArea.NORTH_AMERICA()); |
|
| 310 |
} |
|
| 249 | 311 |
verName.setCreated(null); |
| 250 | 312 |
addOriginalSource(verName, null, null, sourceMap.get(fauEuHelperVernacularName.getSource())); |
| 251 | 313 |
taxonDescription.addElement(verName); |
| ... | ... | |
| 260 | 322 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
| 261 | 323 |
Source source = fauEuConfig.getSource(); |
| 262 | 324 |
TransactionStatus txStatus = null; |
| 263 |
String sourceSelect = "SELECT DISTINCT PESI_FaEu_vernaculars_export.VerSource FROM PESI_FaEu_vernaculars_export group by PESI_FaEu_vernaculars_export.VerSource";
|
|
| 325 |
String sourceSelect = "SELECT DISTINCT vernacularNames.VerSource FROM vernacularNames group by vernacularNames.VerSource";
|
|
| 264 | 326 |
try {
|
| 265 | 327 |
txStatus =startTransaction(); |
| 266 | 328 |
ResultSet rs = source.getResultSet(sourceSelect); |
| ... | ... | |
| 291 | 353 |
String refID = ref.getTitle(); |
| 292 | 354 |
sourceMap.put(refID, ref); |
| 293 | 355 |
} |
| 356 |
|
|
| 294 | 357 |
commitTransaction(txStatus); |
| 295 | 358 |
} |
| 296 | 359 |
} |
Also available in: Unified diff
changes for fauna europaea import