Revision 788f4a81
Added by Andreas Müller over 4 years ago
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiImageExport.java | ||
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/** |
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* Copyright (C) 2009 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.pesi.out.old; |
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import java.net.URI; |
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import java.sql.Connection; |
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import java.sql.PreparedStatement; |
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import java.sql.SQLException; |
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import java.util.List; |
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import java.util.Set; |
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import org.apache.log4j.Logger; |
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportBase; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportState; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.description.TextData; |
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import eu.etaxonomy.cdm.model.media.Media; |
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import eu.etaxonomy.cdm.model.media.MediaRepresentation; |
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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/** |
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* The export class for Images. |
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* Inserts into DataWarehouse database table <code>Image</code>. |
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* @author e.-m.lee |
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* @since 18.08.2010 |
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* |
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*/ |
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@Component |
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public class PesiImageExport extends PesiExportBase { |
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private static final Logger logger = Logger.getLogger(PesiImageExport.class); |
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private static final Class<? extends CdmBase> standardMethodParameter = Reference.class; |
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private static int modCount = 1000; |
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private static final String dbTableName = "Image"; |
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private static final String pluralString = "DescriptionElements"; |
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private static final String parentPluralString = "Taxa"; |
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public PesiImageExport() { |
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super(); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter() |
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*/ |
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@Override |
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public Class<? extends CdmBase> getStandardMethodParameter() { |
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return standardMethodParameter; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected boolean doCheck(PesiExportState state) { |
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boolean result = true; |
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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.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected void doInvoke(PesiExportState state) { |
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logger.error("*** Started Making " + pluralString + " ..."); |
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// Get the limit for objects to save within a single transaction. |
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// int limit = state.getConfig().getLimitSave(); |
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int limit = 1000; |
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// PESI: Clear the database table Image. |
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doDelete(state); |
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// PESI: Create the Images |
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int count = 0; |
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int taxonCount = 0; |
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int pastCount = 0; |
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TransactionStatus txStatus = null; |
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List<TaxonBase> list = null; |
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Connection connection = state.getConfig().getDestination().getConnection(); |
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// Start transaction |
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txStatus = startTransaction(true); |
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
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while ((list = getTaxonService().list(null, limit, taxonCount, null, null)).size() > 0) { |
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taxonCount += list.size(); |
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logger.error("Fetched " + list.size() + " " + parentPluralString + "."); |
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logger.error("Check for Images..."); |
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for (TaxonBase taxonBase : list) { |
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if (taxonBase.isInstanceOf(Taxon.class)) { |
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
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// Determine the TaxonDescriptions |
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Set<TaxonDescription> taxonDescriptions = taxon.getDescriptions(); |
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// Determine the DescriptionElements (Citations) for the current Taxon |
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for (TaxonDescription taxonDescription : taxonDescriptions) { |
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// Check whether this TaxonDescription contains images |
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if (taxonDescription.isImageGallery()) { |
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Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements(); |
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for (DescriptionElementBase descriptionElement : descriptionElements) { |
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if (descriptionElement.isInstanceOf(TextData.class)) { |
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List<Media> media = descriptionElement.getMedia(); |
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for (Media image : media) { |
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Set<MediaRepresentation> representations = image.getRepresentations(); |
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for (MediaRepresentation representation : representations) { |
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List<MediaRepresentationPart> representationParts = representation.getParts(); |
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for (MediaRepresentationPart representationPart : representationParts) { |
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URI mediaUri = representationPart.getUri(); |
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// Add image data |
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String thumb = null; |
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Integer taxonFk = state.getDbId(taxonBase.getName()); |
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if (taxonFk != null && mediaUri != null) { |
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doCount(count++, modCount, pluralString); |
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invokeImages(thumb, mediaUri, taxonFk, connection); |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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logger.error("Exported " + (count - pastCount) + " " + pluralString + "."); |
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// Commit transaction |
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commitTransaction(txStatus); |
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logger.error("Committed transaction."); |
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logger.error("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count); |
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pastCount = count; |
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// Start transaction |
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txStatus = startTransaction(true); |
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
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} |
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if (list.size() == 0) { |
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logger.error("No " + pluralString + " left to fetch."); |
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} |
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// Commit transaction |
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commitTransaction(txStatus); |
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logger.error("Committed transaction."); |
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logger.error("*** Finished Making " + pluralString + " ..." + getSuccessString(true)); |
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return; |
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} |
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/** |
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* Inserts image data into the Image datawarehouse table. |
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* @param thumb |
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* @param url |
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* @param taxonFk |
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* @param connection |
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*/ |
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private void invokeImages(String thumb, URI url, Integer taxonFk, Connection connection) { |
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String imagesSql = "INSERT INTO Image (taxonFk, img_thumb, img_url) VALUES" + |
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" (?, ?, ?)"; |
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try { |
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PreparedStatement imagesStmt = connection.prepareStatement(imagesSql); |
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if (taxonFk != null) { |
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imagesStmt.setInt(1, taxonFk); |
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} else { |
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imagesStmt.setObject(1, null); |
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} |
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if (thumb != null) { |
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imagesStmt.setString(2, thumb); |
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} else { |
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imagesStmt.setObject(2, null); |
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} |
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if (url != null) { |
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imagesStmt.setString(3, url.toString()); |
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} else { |
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imagesStmt.setObject(3, null); |
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} |
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imagesStmt.executeUpdate(); |
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} catch (SQLException e) { |
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logger.error("Image could not be created. TaxonFk: " + taxonFk + ", Thumb: " + thumb + ", URL: " + url); |
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e.printStackTrace(); |
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} |
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} |
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/** |
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* Deletes all entries of database tables related to <code>AdditionalTaxonSource</code>. |
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* @param state The {@link PesiExportState PesiExportState}. |
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* @return Whether the delete operation was successful or not. |
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*/ |
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protected boolean doDelete(PesiExportState state) { |
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PesiExportConfigurator pesiConfig = (PesiExportConfigurator) state.getConfig(); |
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String sql; |
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Source destination = pesiConfig.getDestination(); |
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// Clear AdditionalTaxonSource |
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sql = "DELETE FROM " + dbTableName; |
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destination.setQuery(sql); |
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destination.update(sql); |
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return true; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected boolean isIgnore(PesiExportState state) { |
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return ! ( state.getConfig().isDoImages()); |
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} |
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} |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiImageExport_Old.java | ||
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/** |
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* Copyright (C) 2009 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.pesi.out.old; |
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import java.net.URI; |
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import java.sql.Connection; |
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import java.sql.PreparedStatement; |
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import java.sql.SQLException; |
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import java.util.List; |
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import java.util.Set; |
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import org.apache.log4j.Logger; |
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import org.springframework.stereotype.Component; |
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import org.springframework.transaction.TransactionStatus; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportBase; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
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import eu.etaxonomy.cdm.io.pesi.out.PesiExportState; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.description.TextData; |
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import eu.etaxonomy.cdm.model.media.Media; |
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import eu.etaxonomy.cdm.model.media.MediaRepresentation; |
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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/** |
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* The export class for Images. |
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* Inserts into DataWarehouse database table <code>Image</code>. |
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* @author e.-m.lee |
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* @since 18.08.2010 |
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*/ |
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@Component |
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public class PesiImageExport_Old extends PesiExportBase { |
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private static final long serialVersionUID = 5644950520054486619L; |
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private static final Logger logger = Logger.getLogger(PesiImageExport_Old.class); |
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private static final Class<? extends CdmBase> standardMethodParameter = Reference.class; |
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private static int modCount = 1000; |
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private static final String dbTableName = "Image"; |
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private static final String pluralString = "DescriptionElements"; |
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private static final String parentPluralString = "Taxa"; |
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public PesiImageExport_Old() { |
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super(); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter() |
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*/ |
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@Override |
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public Class<? extends CdmBase> getStandardMethodParameter() { |
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return standardMethodParameter; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected boolean doCheck(PesiExportState state) { |
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boolean result = true; |
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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.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected void doInvoke(PesiExportState state) { |
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logger.error("*** Started Making " + pluralString + " ..."); |
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// Get the limit for objects to save within a single transaction. |
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// int limit = state.getConfig().getLimitSave(); |
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int limit = 1000; |
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// PESI: Clear the database table Image. |
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doDelete(state); |
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// PESI: Create the Images |
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int count = 0; |
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int taxonCount = 0; |
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int pastCount = 0; |
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TransactionStatus txStatus = null; |
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List<TaxonBase> list = null; |
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Connection connection = state.getConfig().getDestination().getConnection(); |
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// Start transaction |
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txStatus = startTransaction(true); |
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
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while ((list = getTaxonService().list(null, limit, taxonCount, null, null)).size() > 0) { |
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taxonCount += list.size(); |
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logger.error("Fetched " + list.size() + " " + parentPluralString + "."); |
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logger.error("Check for Images..."); |
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for (TaxonBase taxonBase : list) { |
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if (taxonBase.isInstanceOf(Taxon.class)) { |
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
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// Determine the TaxonDescriptions |
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Set<TaxonDescription> taxonDescriptions = taxon.getDescriptions(); |
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// Determine the DescriptionElements (Citations) for the current Taxon |
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for (TaxonDescription taxonDescription : taxonDescriptions) { |
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// Check whether this TaxonDescription contains images |
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if (taxonDescription.isImageGallery()) { |
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Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements(); |
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for (DescriptionElementBase descriptionElement : descriptionElements) { |
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if (descriptionElement.isInstanceOf(TextData.class)) { |
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List<Media> media = descriptionElement.getMedia(); |
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for (Media image : media) { |
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Set<MediaRepresentation> representations = image.getRepresentations(); |
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for (MediaRepresentation representation : representations) { |
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List<MediaRepresentationPart> representationParts = representation.getParts(); |
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for (MediaRepresentationPart representationPart : representationParts) { |
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URI mediaUri = representationPart.getUri(); |
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// Add image data |
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String thumb = null; |
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Integer taxonFk = state.getDbId(taxonBase.getName()); |
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if (taxonFk != null && mediaUri != null) { |
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doCount(count++, modCount, pluralString); |
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invokeImages(thumb, mediaUri, taxonFk, connection); |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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} |
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logger.error("Exported " + (count - pastCount) + " " + pluralString + "."); |
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// Commit transaction |
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commitTransaction(txStatus); |
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logger.error("Committed transaction."); |
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logger.error("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count); |
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pastCount = count; |
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// Start transaction |
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txStatus = startTransaction(true); |
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
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} |
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if (list.size() == 0) { |
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logger.error("No " + pluralString + " left to fetch."); |
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} |
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// Commit transaction |
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commitTransaction(txStatus); |
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logger.error("Committed transaction."); |
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logger.error("*** Finished Making " + pluralString + " ..." + getSuccessString(true)); |
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return; |
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} |
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|
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/** |
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* Inserts image data into the Image datawarehouse table. |
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* @param thumb |
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* @param url |
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* @param taxonFk |
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* @param connection |
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*/ |
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private void invokeImages(String thumb, URI url, Integer taxonFk, Connection connection) { |
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String imagesSql = "INSERT INTO Image (taxonFk, img_thumb, img_url) VALUES" + |
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" (?, ?, ?)"; |
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try { |
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PreparedStatement imagesStmt = connection.prepareStatement(imagesSql); |
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|
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if (taxonFk != null) { |
|
198 |
imagesStmt.setInt(1, taxonFk); |
|
199 |
} else { |
|
200 |
imagesStmt.setObject(1, null); |
|
201 |
} |
|
202 |
|
|
203 |
if (thumb != null) { |
|
204 |
imagesStmt.setString(2, thumb); |
|
205 |
} else { |
|
206 |
imagesStmt.setObject(2, null); |
|
207 |
} |
|
208 |
|
|
209 |
if (url != null) { |
|
210 |
imagesStmt.setString(3, url.toString()); |
|
211 |
} else { |
|
212 |
imagesStmt.setObject(3, null); |
|
213 |
} |
|
214 |
|
|
215 |
imagesStmt.executeUpdate(); |
|
216 |
} catch (SQLException e) { |
|
217 |
logger.error("Image could not be created. TaxonFk: " + taxonFk + ", Thumb: " + thumb + ", URL: " + url); |
|
218 |
e.printStackTrace(); |
|
219 |
} |
|
220 |
|
|
221 |
} |
|
222 |
|
|
223 |
/** |
|
224 |
* Deletes all entries of database tables related to <code>AdditionalTaxonSource</code>. |
|
225 |
* @param state The {@link PesiExportState PesiExportState}. |
|
226 |
* @return Whether the delete operation was successful or not. |
|
227 |
*/ |
|
228 |
protected boolean doDelete(PesiExportState state) { |
|
229 |
PesiExportConfigurator pesiConfig = state.getConfig(); |
|
230 |
|
|
231 |
String sql; |
|
232 |
Source destination = pesiConfig.getDestination(); |
|
233 |
|
|
234 |
// Clear AdditionalTaxonSource |
|
235 |
sql = "DELETE FROM " + dbTableName; |
|
236 |
destination.setQuery(sql); |
|
237 |
destination.update(sql); |
|
238 |
return true; |
|
239 |
} |
|
240 |
|
|
241 |
/* (non-Javadoc) |
|
242 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase) |
|
243 |
*/ |
|
244 |
@Override |
|
245 |
protected boolean isIgnore(PesiExportState state) { |
|
246 |
return ! ( state.getConfig().isDoImages()); |
|
247 |
} |
|
248 |
|
|
249 |
} |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2009 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.cdm.io.pesi.out.old; |
|
10 |
|
|
11 |
import java.sql.Connection; |
|
12 |
import java.sql.PreparedStatement; |
|
13 |
import java.sql.SQLException; |
|
14 |
import java.util.Arrays; |
|
15 |
import java.util.List; |
|
16 |
import java.util.Map; |
|
17 |
import java.util.Set; |
|
18 |
|
|
19 |
import org.apache.log4j.Logger; |
|
20 |
import org.joda.time.DateTime; |
|
21 |
import org.springframework.stereotype.Component; |
|
22 |
import org.springframework.transaction.TransactionStatus; |
|
23 |
|
|
24 |
import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
|
25 |
import eu.etaxonomy.cdm.io.common.Source; |
|
26 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
27 |
import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper; |
|
28 |
import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
|
29 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportBase; |
|
30 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
|
31 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportMapping; |
|
32 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportState; |
|
33 |
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
|
34 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
35 |
import eu.etaxonomy.cdm.model.common.Extension; |
|
36 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
|
37 |
import eu.etaxonomy.cdm.model.common.Language; |
|
38 |
import eu.etaxonomy.cdm.model.common.LanguageString; |
|
39 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
40 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
41 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
42 |
import eu.etaxonomy.cdm.model.description.Distribution; |
|
43 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
|
44 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
45 |
import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
|
46 |
import eu.etaxonomy.cdm.model.description.TextData; |
|
47 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
|
48 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
49 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
50 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
51 |
|
|
52 |
/** |
|
53 |
* The export class for {@link eu.etaxonomy.cdm.model.description.DescriptionElementBase DescriptionElements}.<p> |
|
54 |
* Inserts into DataWarehouse database table <code>Note</code>.<p> |
|
55 |
* It is divided into two phases:<ul> |
|
56 |
* <li>Phase 1: Export of DescriptionElements as Notes. |
|
57 |
* <li>Phase 2: Export of TaxonName extensions <code>taxComment</code>, <code>fauComment</code> and <code>fauExtraCodes</code> as Notes.</ul> |
|
58 |
* @author e.-m.lee |
|
59 |
* @since 23.02.2010 |
|
60 |
* |
|
61 |
*/ |
|
62 |
@Component |
|
63 |
public class PesiNoteExport extends PesiExportBase { |
|
64 |
|
|
65 |
private static final long serialVersionUID = 2113856079824112001L; |
|
66 |
private static final Logger logger = Logger.getLogger(PesiNoteExport.class); |
|
67 |
|
|
68 |
private static final Class<? extends CdmBase> standardMethodParameter = DescriptionElementBase.class; |
|
69 |
|
|
70 |
private static int modCount = 1000; |
|
71 |
private static final String dbTableName = "Note"; |
|
72 |
private static final String pluralString = "Notes"; |
|
73 |
private static final String parentPluralString = "Taxa"; |
|
74 |
|
|
75 |
public PesiNoteExport() { |
|
76 |
super(); |
|
77 |
} |
|
78 |
|
|
79 |
@Override |
|
80 |
public Class<? extends CdmBase> getStandardMethodParameter() { |
|
81 |
return standardMethodParameter; |
|
82 |
} |
|
83 |
|
|
84 |
@Override |
|
85 |
protected boolean doCheck(PesiExportState state) { |
|
86 |
boolean result = true; |
|
87 |
return result; |
|
88 |
} |
|
89 |
|
|
90 |
@Override |
|
91 |
protected void doInvoke(PesiExportState state) { |
|
92 |
try { |
|
93 |
logger.info("*** Started Making " + pluralString + " ..."); |
|
94 |
|
|
95 |
// Get the limit for objects to save within a single transaction. |
|
96 |
int limit = state.getConfig().getLimitSave(); |
|
97 |
|
|
98 |
// Stores whether this invoke was successful or not. |
|
99 |
boolean success = true; |
|
100 |
|
|
101 |
// PESI: Clear the database table Note. |
|
102 |
doDelete(state); |
|
103 |
|
|
104 |
// Start transaction |
|
105 |
success &= doPhase01(state); |
|
106 |
|
|
107 |
logger.info("PHASE 2..."); |
|
108 |
doPhase02(state, limit); |
|
109 |
|
|
110 |
logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success)); |
|
111 |
|
|
112 |
if (!success){ |
|
113 |
state.getResult().addError("An error occurred in PesiNoteExport"); |
|
114 |
} |
|
115 |
return; |
|
116 |
} catch (SQLException e) { |
|
117 |
e.printStackTrace(); |
|
118 |
logger.error(e.getMessage()); |
|
119 |
state.getResult().addException(e); |
|
120 |
} |
|
121 |
} |
|
122 |
|
|
123 |
//PHASE 01: Description Elements |
|
124 |
private boolean doPhase01(PesiExportState state) throws SQLException { |
|
125 |
logger.info("PHASE 1..."); |
|
126 |
int count = 0; |
|
127 |
int pastCount = 0; |
|
128 |
boolean success = true; |
|
129 |
|
|
130 |
// Calculate the pageNumber |
|
131 |
int pageNumber = 1; |
|
132 |
int pageSize = 1000; |
|
133 |
|
|
134 |
|
|
135 |
// Get specific mappings: (CDM) DescriptionElement -> (PESI) Note |
|
136 |
PesiExportMapping mapping = getMapping(); |
|
137 |
|
|
138 |
// Initialize the db mapper |
|
139 |
mapping.initialize(state); |
|
140 |
|
|
141 |
|
|
142 |
List<DescriptionElementBase> list = null; |
|
143 |
|
|
144 |
TransactionStatus txStatus = startTransaction(true); |
|
145 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ..."); |
|
146 |
List<String> propPath = Arrays.asList(new String[]{"inDescription.taxon"}); |
|
147 |
while ((list = getDescriptionService().listDescriptionElements(null, null, null, pageSize, pageNumber, propPath)).size() > 0) { |
|
148 |
|
|
149 |
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting..."); |
|
150 |
for (DescriptionElementBase descriptionElement : list) { |
|
151 |
if (getNoteCategoryFk(descriptionElement) != null) { |
|
152 |
doCount(count++, modCount, pluralString); |
|
153 |
success &= mapping.invoke(descriptionElement); |
|
154 |
} |
|
155 |
} |
|
156 |
|
|
157 |
// Commit transaction |
|
158 |
commitTransaction(txStatus); |
|
159 |
logger.debug("Committed transaction."); |
|
160 |
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count); |
|
161 |
pastCount = count; |
|
162 |
|
|
163 |
// Start transaction |
|
164 |
txStatus = startTransaction(true); |
|
165 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ..."); |
|
166 |
|
|
167 |
// Increment pageNumber |
|
168 |
pageNumber++; |
|
169 |
} |
|
170 |
if (list.size() == 0) { |
|
171 |
logger.info("No " + pluralString + " left to fetch."); |
|
172 |
} |
|
173 |
// Commit transaction |
|
174 |
commitTransaction(txStatus); |
|
175 |
logger.info("Committed transaction."); |
|
176 |
return success; |
|
177 |
} |
|
178 |
|
|
179 |
//PHASE 02: Taxa extensions |
|
180 |
private void doPhase02(PesiExportState state, int limit) { |
|
181 |
TransactionStatus txStatus; |
|
182 |
txStatus = startTransaction(true); |
|
183 |
ExtensionType taxCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtTaxComment); |
|
184 |
ExtensionType fauCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauComment); |
|
185 |
ExtensionType fauExtraCodesExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauExtraCodes); |
|
186 |
List<TaxonBase> taxonBaseList = null; |
|
187 |
|
|
188 |
int count = 0; |
|
189 |
int pastCount = 0; |
|
190 |
Connection connection = state.getConfig().getDestination().getConnection(); |
|
191 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
|
192 |
//logger.warn("TODO handle extensions on taxon level, not name level ("); |
|
193 |
while ((taxonBaseList = getTaxonService().list(null, limit, count, null, null)).size() > 0) { |
|
194 |
|
|
195 |
logger.info("Fetched " + taxonBaseList.size() + " names. Exporting..."); |
|
196 |
for (TaxonBase<?> taxon : taxonBaseList) { |
|
197 |
Set<Extension> extensions = taxon.getExtensions(); |
|
198 |
for (Extension extension : extensions) { |
|
199 |
if (extension.getType().equals(taxCommentExtensionType)) { |
|
200 |
String taxComment = extension.getValue(); |
|
201 |
invokeNotes(taxComment, |
|
202 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtTaxComment), |
|
203 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtTaxComment), |
|
204 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
205 |
} else if (extension.getType().equals(fauCommentExtensionType)) { |
|
206 |
String fauComment = extension.getValue(); |
|
207 |
invokeNotes(fauComment, |
|
208 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauComment), |
|
209 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauComment), |
|
210 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
211 |
} else if (extension.getType().equals(fauExtraCodesExtensionType)) { |
|
212 |
String fauExtraCodes = extension.getValue(); |
|
213 |
invokeNotes(fauExtraCodes, |
|
214 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauExtraCodes), |
|
215 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauExtraCodes), |
|
216 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
217 |
} |
|
218 |
} |
|
219 |
|
|
220 |
doCount(count++, modCount, pluralString); |
|
221 |
} |
|
222 |
|
|
223 |
// Commit transaction |
|
224 |
commitTransaction(txStatus); |
|
225 |
logger.debug("Committed transaction."); |
|
226 |
logger.info("Exported " + (count - pastCount) + " names. Total: " + count); |
|
227 |
pastCount = count; |
|
228 |
|
|
229 |
// Start transaction |
|
230 |
txStatus = startTransaction(true); |
|
231 |
logger.info("Started new transaction. Fetching some taxa first (max: " + limit + ") ..."); |
|
232 |
} |
|
233 |
if (taxonBaseList.size() == 0) { |
|
234 |
logger.info("No taxa left to fetch."); |
|
235 |
} |
|
236 |
// Commit transaction |
|
237 |
commitTransaction(txStatus); |
|
238 |
logger.debug("Committed transaction."); |
|
239 |
} |
|
240 |
|
|
241 |
/** |
|
242 |
* @param taxComment |
|
243 |
* @param noteCategoryFk |
|
244 |
* @param noteCategoryCache |
|
245 |
* @param object |
|
246 |
* @param object2 |
|
247 |
*/ |
|
248 |
private void invokeNotes(String note, Integer noteCategoryFk, |
|
249 |
String noteCategoryCache, Integer languageFk, String languageCache, |
|
250 |
Integer taxonFk, Connection connection) { |
|
251 |
String notesSql = "UPDATE Note SET Note_1 = ?, NoteCategoryFk = ?, NoteCategoryCache = ?, LanguageFk = ?, LanguageCache = ? WHERE TaxonFk = ?"; |
|
252 |
try { |
|
253 |
PreparedStatement notesStmt = connection.prepareStatement(notesSql); |
|
254 |
|
|
255 |
if (note != null) { |
|
256 |
notesStmt.setString(1, note); |
|
257 |
} else { |
|
258 |
notesStmt.setObject(1, null); |
|
259 |
} |
|
260 |
|
|
261 |
if (noteCategoryFk != null) { |
|
262 |
notesStmt.setInt(2, noteCategoryFk); |
|
263 |
} else { |
|
264 |
notesStmt.setObject(2, null); |
|
265 |
} |
|
266 |
|
|
267 |
if (noteCategoryCache != null) { |
|
268 |
notesStmt.setString(3, noteCategoryCache); |
|
269 |
} else { |
|
270 |
notesStmt.setObject(3, null); |
|
271 |
} |
|
272 |
|
|
273 |
if (languageFk != null) { |
|
274 |
notesStmt.setInt(4, languageFk); |
|
275 |
} else { |
|
276 |
notesStmt.setObject(4, null); |
|
277 |
} |
|
278 |
|
|
279 |
if (languageCache != null) { |
|
280 |
notesStmt.setString(5, languageCache); |
|
281 |
} else { |
|
282 |
notesStmt.setObject(5, null); |
|
283 |
} |
|
284 |
|
|
285 |
if (taxonFk != null) { |
|
286 |
notesStmt.setInt(6, taxonFk); |
|
287 |
} else { |
|
288 |
notesStmt.setObject(6, null); |
|
289 |
} |
|
290 |
|
|
291 |
notesStmt.executeUpdate(); |
|
292 |
} catch (SQLException e) { |
|
293 |
logger.error("Note could not be created: " + note); |
|
294 |
e.printStackTrace(); |
|
295 |
} |
|
296 |
|
|
297 |
|
|
298 |
} |
|
299 |
|
|
300 |
/** |
|
301 |
* Deletes all entries of database tables related to <code>Note</code>. |
|
302 |
* @param state The PesiExportState |
|
303 |
* @return Whether the delete operation was successful or not. |
|
304 |
*/ |
|
305 |
protected boolean doDelete(PesiExportState state) { |
|
306 |
PesiExportConfigurator pesiConfig = state.getConfig(); |
|
307 |
|
|
308 |
String sql; |
|
309 |
Source destination = pesiConfig.getDestination(); |
|
310 |
|
|
311 |
// Clear NoteSource |
|
312 |
sql = "DELETE FROM NoteSource"; |
|
313 |
destination.setQuery(sql); |
|
314 |
destination.update(sql); |
|
315 |
|
|
316 |
// Clear Note |
|
317 |
sql = "DELETE FROM " + dbTableName; |
|
318 |
destination.setQuery(sql); |
|
319 |
destination.update(sql); |
|
320 |
return true; |
|
321 |
} |
|
322 |
|
|
323 |
@Override |
|
324 |
protected boolean isIgnore(PesiExportState state) { |
|
325 |
return ! state.getConfig().isDoNotes(); |
|
326 |
} |
|
327 |
|
|
328 |
/** |
|
329 |
* Returns the <code>Note_1</code> attribute. |
|
330 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
331 |
* @return The <code>Note_1</code> attribute. |
|
332 |
* @see MethodMapper |
|
333 |
*/ |
|
334 |
@SuppressWarnings("unused") |
|
335 |
private static String getNote_1(DescriptionElementBase descriptionElement) { |
|
336 |
String result = null; |
|
337 |
|
|
338 |
if (descriptionElement.isInstanceOf(TextData.class)) { |
|
339 |
TextData textData = CdmBase.deproxy(descriptionElement, TextData.class); |
|
340 |
result = textData.getText(Language.DEFAULT()); |
|
341 |
} |
|
342 |
|
|
343 |
return result; |
|
344 |
} |
|
345 |
|
|
346 |
/** |
|
347 |
* Returns the <code>Note_2</code> attribute. |
|
348 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
349 |
* @return The <code>Note_2</code> attribute. |
|
350 |
* @see MethodMapper |
|
351 |
*/ |
|
352 |
@SuppressWarnings("unused") |
|
353 |
private static String getNote_2(DescriptionElementBase descriptionElement) { |
|
354 |
logger.warn("Not yet implemented"); |
|
355 |
return null; |
|
356 |
} |
|
357 |
|
|
358 |
/** |
|
359 |
* Returns the <code>NoteCategoryFk</code> attribute. |
|
360 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
361 |
* @return The <code>NoteCategoryFk</code> attribute. |
|
362 |
* @see MethodMapper |
|
363 |
*/ |
|
364 |
private static Integer getNoteCategoryFk(DescriptionElementBase descriptionElement) { |
|
365 |
Integer result = null; |
|
366 |
result = PesiTransformer.feature2NoteCategoryFk(descriptionElement.getFeature()); |
|
367 |
return result; |
|
368 |
} |
|
369 |
|
|
370 |
/** |
|
371 |
* Returns the <code>NoteCategoryCache</code> attribute. |
|
372 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
373 |
* @return The <code>NoteCategoryCache</code> attribute. |
|
374 |
* @see MethodMapper |
|
375 |
*/ |
|
376 |
@SuppressWarnings("unused") |
|
377 |
private static String getNoteCategoryCache(DescriptionElementBase descriptionElement, PesiExportState state) { |
|
378 |
return state.getTransformer().getCacheByFeature(descriptionElement.getFeature()); |
|
379 |
} |
|
380 |
|
|
381 |
/** |
|
382 |
* Returns the <code>LanguageFk</code> attribute. |
|
383 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
384 |
* @return The <code>LanguageFk</code> attribute. |
|
385 |
* @see MethodMapper |
|
386 |
*/ |
|
387 |
@SuppressWarnings("unused") |
|
388 |
private static Integer getLanguageFk(DescriptionElementBase descriptionElement) { |
|
389 |
Language language = getLanguage(descriptionElement); |
|
390 |
|
|
391 |
return PesiTransformer.language2LanguageId(language); |
|
392 |
} |
|
393 |
|
|
394 |
/** |
|
395 |
* Returns the <code>LanguageCache</code> attribute. |
|
396 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
397 |
* @return The <code>LanguageCache</code> attribute. |
|
398 |
* @throws UndefinedTransformerMethodException |
|
399 |
* @see MethodMapper |
|
400 |
*/ |
|
401 |
@SuppressWarnings("unused") |
|
402 |
private static String getLanguageCache(DescriptionElementBase descriptionElement, PesiExportState state) throws UndefinedTransformerMethodException { |
|
403 |
Language language = getLanguage(descriptionElement); |
|
404 |
return state.getTransformer().getCacheByLanguage(language); |
|
405 |
} |
|
406 |
|
|
407 |
private static Language getLanguage(DescriptionElementBase descriptionElement) { |
|
408 |
Language language = null; |
|
409 |
|
|
410 |
Map<Language, LanguageString> multilanguageText = null; |
|
411 |
if (descriptionElement.isInstanceOf(CommonTaxonName.class)) { |
|
412 |
CommonTaxonName commonTaxonName = CdmBase.deproxy(descriptionElement, CommonTaxonName.class); |
|
413 |
language = commonTaxonName.getLanguage(); |
|
414 |
} else if (descriptionElement.isInstanceOf(TextData.class)) { |
|
415 |
TextData textData = CdmBase.deproxy(descriptionElement, TextData.class); |
|
416 |
multilanguageText = textData.getMultilanguageText(); |
|
417 |
} else if (descriptionElement.isInstanceOf(IndividualsAssociation.class)) { |
|
418 |
IndividualsAssociation individualsAssociation = CdmBase.deproxy(descriptionElement, IndividualsAssociation.class); |
|
419 |
multilanguageText = individualsAssociation.getDescription(); |
|
420 |
} else if (descriptionElement.isInstanceOf(TaxonInteraction.class)) { |
|
421 |
TaxonInteraction taxonInteraction = CdmBase.deproxy(descriptionElement, TaxonInteraction.class); |
|
422 |
multilanguageText = taxonInteraction.getDescription(); |
|
423 |
} else { |
|
424 |
logger.debug("Given descriptionElement does not support languages. Hence LanguageCache could not be determined: " + descriptionElement.getUuid()); |
|
425 |
} |
|
426 |
|
|
427 |
if (multilanguageText != null) { |
|
428 |
Set<Language> languages = multilanguageText.keySet(); |
|
429 |
|
|
430 |
// TODO: Think of something more sophisticated than this |
|
431 |
if (languages.size() > 0) { |
|
432 |
language = languages.iterator().next(); |
|
433 |
} |
|
434 |
if (languages.size() > 1){ |
|
435 |
logger.warn("There is more than 1 language for a given description (" + descriptionElement.getClass().getSimpleName() + "):" + descriptionElement.getUuid()); |
|
436 |
} |
|
437 |
} |
|
438 |
return language; |
|
439 |
} |
|
440 |
|
|
441 |
/** |
|
442 |
* Returns the <code>Region</code> attribute. |
|
443 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
444 |
* @return The <code>Region</code> attribute. |
|
445 |
* @see MethodMapper |
|
446 |
*/ |
|
447 |
@SuppressWarnings("unused") |
|
448 |
private static String getRegion(DescriptionElementBase descriptionElement) { |
|
449 |
String result = null; |
|
450 |
DescriptionBase<?> inDescription = descriptionElement.getInDescription(); |
|
451 |
|
|
452 |
try { |
|
453 |
// Area information are associated to TaxonDescriptions and Distributions. |
|
454 |
if (descriptionElement.isInstanceOf(Distribution.class)) { |
|
455 |
Distribution distribution = CdmBase.deproxy(descriptionElement, Distribution.class); |
|
456 |
//TODO not working any more after transformer refactoring |
|
457 |
result = new PesiTransformer(null).getCacheByNamedArea(distribution.getArea()); |
|
458 |
} else if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) { |
|
459 |
TaxonDescription taxonDescription = CdmBase.deproxy(inDescription, TaxonDescription.class); |
|
460 |
Set<NamedArea> namedAreas = taxonDescription.getGeoScopes(); |
|
461 |
if (namedAreas.size() == 1) { |
|
462 |
result = new PesiTransformer(null).getCacheByNamedArea(namedAreas.iterator().next()); |
|
463 |
} else if (namedAreas.size() > 1) { |
|
464 |
logger.warn("This TaxonDescription contains more than one NamedArea: " + taxonDescription.getTitleCache()); |
|
465 |
} |
|
466 |
} |
|
467 |
} catch (ClassCastException e) { |
|
468 |
// TODO Auto-generated catch block |
|
469 |
e.printStackTrace(); |
|
470 |
} catch (UndefinedTransformerMethodException e) { |
|
471 |
// TODO Auto-generated catch block |
|
472 |
e.printStackTrace(); |
|
473 |
} |
|
474 |
return result; |
|
475 |
} |
|
476 |
|
|
477 |
/** |
|
478 |
* Returns the <code>TaxonFk</code> attribute. |
|
479 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
480 |
* @param state The {@link PesiExportState PesiExportState}. |
|
481 |
* @return The <code>TaxonFk</code> attribute. |
|
482 |
* @see MethodMapper |
|
483 |
*/ |
|
484 |
@SuppressWarnings("unused") |
|
485 |
private static Integer getTaxonFk(DescriptionElementBase descriptionElement, DbExportStateBase<?, PesiTransformer> state) { |
|
486 |
Integer result = null; |
|
487 |
DescriptionBase<?> inDescription = descriptionElement.getInDescription(); |
|
488 |
if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) { |
|
489 |
TaxonDescription taxonDescription = CdmBase.deproxy(inDescription, TaxonDescription.class); |
|
490 |
Taxon taxon = taxonDescription.getTaxon(); |
|
491 |
result = state.getDbId(taxon.getName()); |
|
492 |
} |
|
493 |
return result; |
|
494 |
} |
|
495 |
|
|
496 |
/** |
|
497 |
* Returns the TaxonFk for a given TaxonName. |
|
498 |
* @param taxonName The {@link TaxonNameBase TaxonName}. |
|
499 |
* @param state The {@link DbExportStateBase DbExportState}. |
|
500 |
* @return |
|
501 |
*/ |
|
502 |
private static Integer getTaxonFk(TaxonName taxonName, DbExportStateBase<?, PesiTransformer> state) { |
|
503 |
return state.getDbId(taxonName); |
|
504 |
} |
|
505 |
|
|
506 |
/** |
|
507 |
* Returns the <code>LastAction</code> attribute. |
|
508 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
509 |
* @return The <code>LastAction</code> attribute. |
|
510 |
* @see MethodMapper |
|
511 |
*/ |
|
512 |
@SuppressWarnings("unused") |
|
513 |
private static String getLastAction(DescriptionElementBase descriptionElement) { |
|
514 |
// TODO |
|
515 |
return null; |
|
516 |
} |
|
517 |
|
|
518 |
/** |
|
519 |
* Returns the <code>LastActionDate</code> attribute. |
|
520 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
521 |
* @return The <code>LastActionDate</code> attribute. |
|
522 |
* @see MethodMapper |
|
523 |
*/ |
|
524 |
@SuppressWarnings("unused") |
|
525 |
private static DateTime getLastActionDate(DescriptionElementBase descriptionElement) { |
|
526 |
DateTime result = null; |
|
527 |
return result; |
|
528 |
} |
|
529 |
|
|
530 |
/** |
|
531 |
* Returns the CDM to PESI specific export mappings. |
|
532 |
* @return The {@link PesiExportMapping PesiExportMapping}. |
|
533 |
*/ |
|
534 |
private PesiExportMapping getMapping() { |
|
535 |
PesiExportMapping mapping = new PesiExportMapping(dbTableName); |
|
536 |
|
|
537 |
mapping.addMapper(IdMapper.NewInstance("NoteId")); |
|
538 |
mapping.addMapper(MethodMapper.NewInstance("Note_1", this)); |
|
539 |
mapping.addMapper(MethodMapper.NewInstance("Note_2", this)); |
|
540 |
mapping.addMapper(MethodMapper.NewInstance("NoteCategoryFk", this)); |
|
541 |
mapping.addMapper(MethodMapper.NewInstance("NoteCategoryCache", this)); |
|
542 |
mapping.addMapper(MethodMapper.NewInstance("LanguageFk", this)); |
|
543 |
mapping.addMapper(MethodMapper.NewInstance("LanguageCache", this)); |
|
544 |
mapping.addMapper(MethodMapper.NewInstance("Region", this)); |
|
545 |
mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this.getClass(), "getTaxonFk", standardMethodParameter, DbExportStateBase.class)); |
|
546 |
mapping.addMapper(MethodMapper.NewInstance("LastAction", this)); |
|
547 |
mapping.addMapper(MethodMapper.NewInstance("LastActionDate", this)); |
|
548 |
|
|
549 |
return mapping; |
|
550 |
} |
|
551 |
|
|
552 |
} |
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/old/PesiNoteExport_Old.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2009 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.cdm.io.pesi.out.old; |
|
10 |
|
|
11 |
import java.sql.Connection; |
|
12 |
import java.sql.PreparedStatement; |
|
13 |
import java.sql.SQLException; |
|
14 |
import java.util.Arrays; |
|
15 |
import java.util.List; |
|
16 |
import java.util.Map; |
|
17 |
import java.util.Set; |
|
18 |
|
|
19 |
import org.apache.log4j.Logger; |
|
20 |
import org.joda.time.DateTime; |
|
21 |
import org.springframework.stereotype.Component; |
|
22 |
import org.springframework.transaction.TransactionStatus; |
|
23 |
|
|
24 |
import eu.etaxonomy.cdm.io.common.DbExportStateBase; |
|
25 |
import eu.etaxonomy.cdm.io.common.Source; |
|
26 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
27 |
import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper; |
|
28 |
import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
|
29 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportBase; |
|
30 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportConfigurator; |
|
31 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportMapping; |
|
32 |
import eu.etaxonomy.cdm.io.pesi.out.PesiExportState; |
|
33 |
import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer; |
|
34 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
35 |
import eu.etaxonomy.cdm.model.common.Extension; |
|
36 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
|
37 |
import eu.etaxonomy.cdm.model.common.Language; |
|
38 |
import eu.etaxonomy.cdm.model.common.LanguageString; |
|
39 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
|
40 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
41 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
42 |
import eu.etaxonomy.cdm.model.description.Distribution; |
|
43 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
|
44 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
45 |
import eu.etaxonomy.cdm.model.description.TaxonInteraction; |
|
46 |
import eu.etaxonomy.cdm.model.description.TextData; |
|
47 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
|
48 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
49 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
50 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
51 |
|
|
52 |
/** |
|
53 |
* The export class for {@link eu.etaxonomy.cdm.model.description.DescriptionElementBase DescriptionElements}.<p> |
|
54 |
* Inserts into DataWarehouse database table <code>Note</code>.<p> |
|
55 |
* It is divided into two phases:<ul> |
|
56 |
* <li>Phase 1: Export of DescriptionElements as Notes. |
|
57 |
* <li>Phase 2: Export of TaxonName extensions <code>taxComment</code>, <code>fauComment</code> and <code>fauExtraCodes</code> as Notes.</ul> |
|
58 |
* @author e.-m.lee |
|
59 |
* @since 23.02.2010 |
|
60 |
*/ |
|
61 |
@Component |
|
62 |
public class PesiNoteExport_Old extends PesiExportBase { |
|
63 |
|
|
64 |
private static final long serialVersionUID = 2113856079824112001L; |
|
65 |
private static final Logger logger = Logger.getLogger(PesiNoteExport_Old.class); |
|
66 |
|
|
67 |
private static final Class<? extends CdmBase> standardMethodParameter = DescriptionElementBase.class; |
|
68 |
|
|
69 |
private static int modCount = 1000; |
|
70 |
private static final String dbTableName = "Note"; |
|
71 |
private static final String pluralString = "Notes"; |
|
72 |
private static final String parentPluralString = "Taxa"; |
|
73 |
|
|
74 |
public PesiNoteExport_Old() { |
|
75 |
super(); |
|
76 |
} |
|
77 |
|
|
78 |
@Override |
|
79 |
public Class<? extends CdmBase> getStandardMethodParameter() { |
|
80 |
return standardMethodParameter; |
|
81 |
} |
|
82 |
|
|
83 |
@Override |
|
84 |
protected boolean doCheck(PesiExportState state) { |
|
85 |
boolean result = true; |
|
86 |
return result; |
|
87 |
} |
|
88 |
|
|
89 |
@Override |
|
90 |
protected void doInvoke(PesiExportState state) { |
|
91 |
try { |
|
92 |
logger.info("*** Started Making " + pluralString + " ..."); |
|
93 |
|
|
94 |
// Get the limit for objects to save within a single transaction. |
|
95 |
int limit = state.getConfig().getLimitSave(); |
|
96 |
|
|
97 |
// Stores whether this invoke was successful or not. |
|
98 |
boolean success = true; |
|
99 |
|
|
100 |
// PESI: Clear the database table Note. |
|
101 |
doDelete(state); |
|
102 |
|
|
103 |
// Start transaction |
|
104 |
success &= doPhase01(state); |
|
105 |
|
|
106 |
logger.info("PHASE 2..."); |
|
107 |
doPhase02(state, limit); |
|
108 |
|
|
109 |
logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success)); |
|
110 |
|
|
111 |
if (!success){ |
|
112 |
state.getResult().addError("An error occurred in PesiNoteExport"); |
|
113 |
} |
|
114 |
return; |
|
115 |
} catch (SQLException e) { |
|
116 |
e.printStackTrace(); |
|
117 |
logger.error(e.getMessage()); |
|
118 |
state.getResult().addException(e); |
|
119 |
} |
|
120 |
} |
|
121 |
|
|
122 |
//PHASE 01: Description Elements |
|
123 |
private boolean doPhase01(PesiExportState state) throws SQLException { |
|
124 |
logger.info("PHASE 1..."); |
|
125 |
int count = 0; |
|
126 |
int pastCount = 0; |
|
127 |
boolean success = true; |
|
128 |
|
|
129 |
// Calculate the pageNumber |
|
130 |
int pageNumber = 1; |
|
131 |
int pageSize = 1000; |
|
132 |
|
|
133 |
|
|
134 |
// Get specific mappings: (CDM) DescriptionElement -> (PESI) Note |
|
135 |
PesiExportMapping mapping = getMapping(); |
|
136 |
|
|
137 |
// Initialize the db mapper |
|
138 |
mapping.initialize(state); |
|
139 |
|
|
140 |
|
|
141 |
List<DescriptionElementBase> list = null; |
|
142 |
|
|
143 |
TransactionStatus txStatus = startTransaction(true); |
|
144 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ..."); |
|
145 |
List<String> propPath = Arrays.asList(new String[]{"inDescription.taxon"}); |
|
146 |
while ((list = getDescriptionService().listDescriptionElements(null, null, null, pageSize, pageNumber, propPath)).size() > 0) { |
|
147 |
|
|
148 |
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting..."); |
|
149 |
for (DescriptionElementBase descriptionElement : list) { |
|
150 |
if (getNoteCategoryFk(descriptionElement) != null) { |
|
151 |
doCount(count++, modCount, pluralString); |
|
152 |
success &= mapping.invoke(descriptionElement); |
|
153 |
} |
|
154 |
} |
|
155 |
|
|
156 |
// Commit transaction |
|
157 |
commitTransaction(txStatus); |
|
158 |
logger.debug("Committed transaction."); |
|
159 |
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count); |
|
160 |
pastCount = count; |
|
161 |
|
|
162 |
// Start transaction |
|
163 |
txStatus = startTransaction(true); |
|
164 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + pageSize + ") ..."); |
|
165 |
|
|
166 |
// Increment pageNumber |
|
167 |
pageNumber++; |
|
168 |
} |
|
169 |
if (list.size() == 0) { |
|
170 |
logger.info("No " + pluralString + " left to fetch."); |
|
171 |
} |
|
172 |
// Commit transaction |
|
173 |
commitTransaction(txStatus); |
|
174 |
logger.info("Committed transaction."); |
|
175 |
return success; |
|
176 |
} |
|
177 |
|
|
178 |
//PHASE 02: Taxa extensions |
|
179 |
private void doPhase02(PesiExportState state, int limit) { |
|
180 |
TransactionStatus txStatus; |
|
181 |
txStatus = startTransaction(true); |
|
182 |
ExtensionType taxCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtTaxComment); |
|
183 |
ExtensionType fauCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauComment); |
|
184 |
ExtensionType fauExtraCodesExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauExtraCodes); |
|
185 |
List<TaxonBase> taxonBaseList = null; |
|
186 |
|
|
187 |
int count = 0; |
|
188 |
int pastCount = 0; |
|
189 |
Connection connection = state.getConfig().getDestination().getConnection(); |
|
190 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ..."); |
|
191 |
//logger.warn("TODO handle extensions on taxon level, not name level ("); |
|
192 |
while ((taxonBaseList = getTaxonService().list(null, limit, count, null, null)).size() > 0) { |
|
193 |
|
|
194 |
logger.info("Fetched " + taxonBaseList.size() + " names. Exporting..."); |
|
195 |
for (TaxonBase<?> taxon : taxonBaseList) { |
|
196 |
Set<Extension> extensions = taxon.getExtensions(); |
|
197 |
for (Extension extension : extensions) { |
|
198 |
if (extension.getType().equals(taxCommentExtensionType)) { |
|
199 |
String taxComment = extension.getValue(); |
|
200 |
invokeNotes(taxComment, |
|
201 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtTaxComment), |
|
202 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtTaxComment), |
|
203 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
204 |
} else if (extension.getType().equals(fauCommentExtensionType)) { |
|
205 |
String fauComment = extension.getValue(); |
|
206 |
invokeNotes(fauComment, |
|
207 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauComment), |
|
208 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauComment), |
|
209 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
210 |
} else if (extension.getType().equals(fauExtraCodesExtensionType)) { |
|
211 |
String fauExtraCodes = extension.getValue(); |
|
212 |
invokeNotes(fauExtraCodes, |
|
213 |
PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauExtraCodes), |
|
214 |
PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauExtraCodes), |
|
215 |
null, null, getTaxonFk(taxon.getName(), state),connection); |
|
216 |
} |
|
217 |
} |
|
218 |
|
|
219 |
doCount(count++, modCount, pluralString); |
|
220 |
} |
|
221 |
|
|
222 |
// Commit transaction |
|
223 |
commitTransaction(txStatus); |
|
224 |
logger.debug("Committed transaction."); |
|
225 |
logger.info("Exported " + (count - pastCount) + " names. Total: " + count); |
|
226 |
pastCount = count; |
|
227 |
|
|
228 |
// Start transaction |
|
229 |
txStatus = startTransaction(true); |
|
230 |
logger.info("Started new transaction. Fetching some taxa first (max: " + limit + ") ..."); |
|
231 |
} |
|
232 |
if (taxonBaseList.size() == 0) { |
|
233 |
logger.info("No taxa left to fetch."); |
|
234 |
} |
|
235 |
// Commit transaction |
|
236 |
commitTransaction(txStatus); |
|
237 |
logger.debug("Committed transaction."); |
|
238 |
} |
|
239 |
|
|
240 |
/** |
|
241 |
* @param taxComment |
|
242 |
* @param noteCategoryFk |
|
243 |
* @param noteCategoryCache |
|
244 |
* @param object |
|
245 |
* @param object2 |
|
246 |
*/ |
|
247 |
private void invokeNotes(String note, Integer noteCategoryFk, |
|
248 |
String noteCategoryCache, Integer languageFk, String languageCache, |
|
249 |
Integer taxonFk, Connection connection) { |
|
250 |
String notesSql = "UPDATE Note SET Note_1 = ?, NoteCategoryFk = ?, NoteCategoryCache = ?, LanguageFk = ?, LanguageCache = ? WHERE TaxonFk = ?"; |
|
251 |
try { |
|
252 |
PreparedStatement notesStmt = connection.prepareStatement(notesSql); |
|
253 |
|
|
254 |
if (note != null) { |
|
255 |
notesStmt.setString(1, note); |
|
256 |
} else { |
|
257 |
notesStmt.setObject(1, null); |
|
258 |
} |
|
259 |
|
|
260 |
if (noteCategoryFk != null) { |
|
261 |
notesStmt.setInt(2, noteCategoryFk); |
|
262 |
} else { |
|
263 |
notesStmt.setObject(2, null); |
|
264 |
} |
|
265 |
|
|
266 |
if (noteCategoryCache != null) { |
|
267 |
notesStmt.setString(3, noteCategoryCache); |
|
268 |
} else { |
|
269 |
notesStmt.setObject(3, null); |
|
270 |
} |
|
271 |
|
|
272 |
if (languageFk != null) { |
|
273 |
notesStmt.setInt(4, languageFk); |
|
274 |
} else { |
|
275 |
notesStmt.setObject(4, null); |
|
276 |
} |
|
277 |
|
|
278 |
if (languageCache != null) { |
|
279 |
notesStmt.setString(5, languageCache); |
|
280 |
} else { |
|
281 |
notesStmt.setObject(5, null); |
|
282 |
} |
|
283 |
|
|
284 |
if (taxonFk != null) { |
|
285 |
notesStmt.setInt(6, taxonFk); |
|
286 |
} else { |
|
287 |
notesStmt.setObject(6, null); |
|
288 |
} |
|
289 |
|
|
290 |
notesStmt.executeUpdate(); |
|
291 |
} catch (SQLException e) { |
|
292 |
logger.error("Note could not be created: " + note); |
|
293 |
e.printStackTrace(); |
|
294 |
} |
|
295 |
|
|
296 |
|
|
297 |
} |
|
298 |
|
|
299 |
/** |
|
300 |
* Deletes all entries of database tables related to <code>Note</code>. |
|
301 |
* @param state The PesiExportState |
|
302 |
* @return Whether the delete operation was successful or not. |
|
303 |
*/ |
|
304 |
protected boolean doDelete(PesiExportState state) { |
|
305 |
PesiExportConfigurator pesiConfig = state.getConfig(); |
|
306 |
|
|
307 |
String sql; |
|
308 |
Source destination = pesiConfig.getDestination(); |
|
309 |
|
|
310 |
// Clear NoteSource |
|
311 |
sql = "DELETE FROM NoteSource"; |
|
312 |
destination.setQuery(sql); |
|
313 |
destination.update(sql); |
|
314 |
|
|
315 |
// Clear Note |
|
316 |
sql = "DELETE FROM " + dbTableName; |
|
317 |
destination.setQuery(sql); |
|
318 |
destination.update(sql); |
|
319 |
return true; |
|
320 |
} |
|
321 |
|
|
322 |
@Override |
|
323 |
protected boolean isIgnore(PesiExportState state) { |
|
324 |
return ! state.getConfig().isDoNotes(); |
|
325 |
} |
|
326 |
|
|
327 |
/** |
|
328 |
* Returns the <code>Note_1</code> attribute. |
|
329 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
330 |
* @return The <code>Note_1</code> attribute. |
|
331 |
* @see MethodMapper |
|
332 |
*/ |
|
333 |
@SuppressWarnings("unused") |
|
334 |
private static String getNote_1(DescriptionElementBase descriptionElement) { |
|
335 |
String result = null; |
|
336 |
|
|
337 |
if (descriptionElement.isInstanceOf(TextData.class)) { |
|
338 |
TextData textData = CdmBase.deproxy(descriptionElement, TextData.class); |
|
339 |
result = textData.getText(Language.DEFAULT()); |
|
340 |
} |
|
341 |
|
|
342 |
return result; |
|
343 |
} |
|
344 |
|
|
345 |
/** |
|
346 |
* Returns the <code>Note_2</code> attribute. |
|
347 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
348 |
* @return The <code>Note_2</code> attribute. |
|
349 |
* @see MethodMapper |
|
350 |
*/ |
|
351 |
@SuppressWarnings("unused") |
|
352 |
private static String getNote_2(DescriptionElementBase descriptionElement) { |
|
353 |
logger.warn("Not yet implemented"); |
|
354 |
return null; |
|
355 |
} |
|
356 |
|
|
357 |
/** |
|
358 |
* Returns the <code>NoteCategoryFk</code> attribute. |
|
359 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
360 |
* @return The <code>NoteCategoryFk</code> attribute. |
|
361 |
* @see MethodMapper |
|
362 |
*/ |
|
363 |
private static Integer getNoteCategoryFk(DescriptionElementBase descriptionElement) { |
|
364 |
Integer result = null; |
|
365 |
result = PesiTransformer.feature2NoteCategoryFk(descriptionElement.getFeature()); |
|
366 |
return result; |
|
367 |
} |
|
368 |
|
|
369 |
/** |
|
370 |
* Returns the <code>NoteCategoryCache</code> attribute. |
|
371 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
372 |
* @return The <code>NoteCategoryCache</code> attribute. |
|
373 |
* @see MethodMapper |
|
374 |
*/ |
|
375 |
@SuppressWarnings("unused") |
|
376 |
private static String getNoteCategoryCache(DescriptionElementBase descriptionElement, PesiExportState state) { |
|
377 |
return state.getTransformer().getCacheByFeature(descriptionElement.getFeature()); |
|
378 |
} |
|
379 |
|
|
380 |
/** |
|
381 |
* Returns the <code>LanguageFk</code> attribute. |
|
382 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
383 |
* @return The <code>LanguageFk</code> attribute. |
|
384 |
* @see MethodMapper |
|
385 |
*/ |
|
386 |
@SuppressWarnings("unused") |
|
387 |
private static Integer getLanguageFk(DescriptionElementBase descriptionElement) { |
|
388 |
Language language = getLanguage(descriptionElement); |
|
389 |
|
|
390 |
return PesiTransformer.language2LanguageId(language); |
|
391 |
} |
|
392 |
|
|
393 |
/** |
|
394 |
* Returns the <code>LanguageCache</code> attribute. |
|
395 |
* @param descriptionElement The {@link DescriptionElementBase DescriptionElement}. |
|
396 |
* @return The <code>LanguageCache</code> attribute. |
|
397 |
* @throws UndefinedTransformerMethodException |
|
398 |
* @see MethodMapper |
|
399 |
*/ |
|
400 |
@SuppressWarnings("unused") |
|
401 |
private static String getLanguageCache(DescriptionElementBase descriptionElement, PesiExportState state) throws UndefinedTransformerMethodException { |
|
402 |
Language language = getLanguage(descriptionElement); |
|
403 |
return state.getTransformer().getCacheByLanguage(language); |
|
404 |
} |
|
405 |
|
|
406 |
private static Language getLanguage(DescriptionElementBase descriptionElement) { |
|
407 |
Language language = null; |
|
408 |
|
|
409 |
Map<Language, LanguageString> multilanguageText = null; |
|
410 |
if (descriptionElement.isInstanceOf(CommonTaxonName.class)) { |
|
411 |
CommonTaxonName commonTaxonName = CdmBase.deproxy(descriptionElement, CommonTaxonName.class); |
|
412 |
language = commonTaxonName.getLanguage(); |
|
413 |
} else if (descriptionElement.isInstanceOf(TextData.class)) { |
|
414 |
TextData textData = CdmBase.deproxy(descriptionElement, TextData.class); |
|
415 |
multilanguageText = textData.getMultilanguageText(); |
|
416 |
} else if (descriptionElement.isInstanceOf(IndividualsAssociation.class)) { |
|
417 |
IndividualsAssociation individualsAssociation = CdmBase.deproxy(descriptionElement, IndividualsAssociation.class); |
|
418 |
multilanguageText = individualsAssociation.getDescription(); |
|
419 |
} else if (descriptionElement.isInstanceOf(TaxonInteraction.class)) { |
|
420 |
TaxonInteraction taxonInteraction = CdmBase.deproxy(descriptionElement, TaxonInteraction.class); |
|
421 |
multilanguageText = taxonInteraction.getDescription(); |
|
422 |
} else { |
|
423 |
logger.debug("Given descriptionElement does not support languages. Hence LanguageCache could not be determined: " + descriptionElement.getUuid()); |
Also available in: Unified diff
ref #8509 rename old PESI factual data exports