Revision 6243a668
Added by Andreas Müller over 11 years ago
| .gitattributes | ||
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| 98 | 98 |
app-import/src/main/java/eu/etaxonomy/cdm/io/PalmaeImageImport.java -text |
| 99 | 99 |
app-import/src/main/java/eu/etaxonomy/cdm/io/PalmaeProtologueImport.java -text |
| 100 | 100 |
app-import/src/main/java/eu/etaxonomy/cdm/io/ProtologueImport.java -text |
| 101 |
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraCollectionImport.java -text |
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| 101 | 102 |
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportConfigurator.java -text |
| 102 | 103 |
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportState.java -text |
| 103 | 104 |
app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportTransformer.java -text |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraCollectionImport.java | ||
|---|---|---|
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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package eu.etaxonomy.cdm.io.algaterra; |
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import java.sql.ResultSet; |
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import java.sql.SQLException; |
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import java.util.HashMap; |
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import java.util.HashSet; |
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import java.util.Map; |
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import java.util.Set; |
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import java.util.UUID; |
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import org.apache.commons.lang.StringUtils; |
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import org.apache.log4j.Logger; |
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import org.springframework.stereotype.Component; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType; |
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException; |
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraCollectionImportValidator; |
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState; |
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport; |
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import eu.etaxonomy.cdm.io.common.IOValidator; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.Language; |
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import eu.etaxonomy.cdm.model.common.Marker; |
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import eu.etaxonomy.cdm.model.common.MarkerType; |
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import eu.etaxonomy.cdm.model.common.TermVocabulary; |
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import eu.etaxonomy.cdm.model.description.CategoricalData; |
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import eu.etaxonomy.cdm.model.description.DescriptionBase; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.MeasurementUnit; |
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import eu.etaxonomy.cdm.model.description.Modifier; |
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import eu.etaxonomy.cdm.model.description.QuantitativeData; |
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import eu.etaxonomy.cdm.model.description.State; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
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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.name.BotanicalName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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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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* @author a.mueller |
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* @created 01.09.2012 |
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*/ |
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@Component |
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public class AlgaTerraCollectionImport extends AlgaTerraSpecimenImportBase {
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private static final Logger logger = Logger.getLogger(AlgaTerraCollectionImport.class); |
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private static int modCount = 5000; |
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private static final String pluralString = "collections"; |
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private static final String dbTableName = "Collection"; //?? |
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public static final String NAMESPACE_COLLECTION = "Collection"; |
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public static final String NAMESPACE_SUBCOLLECTION = "Collection (Subcollection)"; |
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public AlgaTerraCollectionImport(){
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super(); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery() |
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*/ |
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@Override |
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protected String getIdQuery(BerlinModelImportState state) {
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String result = " SELECT CollectionId " + |
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" FROM Collection c " |
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+ " ORDER BY c.CollectionId "; |
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return result; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator) |
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*/ |
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@Override |
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = |
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" SELECT CollectionId, Name, Town, IHCode, Subcollection, TDWGGazetteerFk, Address, CultCollFlag, " + |
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" Created_When, Updated_When, Created_Who, Updated_Who, Notes " + |
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" FROM Collection c " + |
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" WHERE c.CollectionId IN (" + ID_LIST_TOKEN + ") "
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+ " ORDER BY c.CollectionId " |
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; |
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return strQuery; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState) |
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*/ |
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
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boolean success = true; |
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AlgaTerraImportState state = (AlgaTerraImportState)bmState; |
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Set<Collection> collectionsToSave = new HashSet<Collection>(); |
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ResultSet rs = partitioner.getResultSet(); |
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try {
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int i = 0; |
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//for each reference |
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
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int collectionId = rs.getInt("CollectionId");
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String name = rs.getString("Name");
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String town = rs.getString("Town");
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String ihCode = rs.getString("IHCode");
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String subCollectionStr = rs.getString("Subcollection");
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Integer tdwgArea = nullSafeInt(rs, "TDWGGazetteerFk"); //somehow redundant with town |
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String address = rs.getString("Address"); //only available for BGBM
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Boolean cultCollFlag = rs.getBoolean("CultCollFlag"); //?? not really needed according to Henning
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//TODO createdUpdates, NOtes |
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try {
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//source ref |
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Reference<?> sourceRef = state.getTransactionalSourceReference(); |
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Collection collection = Collection.NewInstance(); |
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collection.setName(name); |
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if (isNotBlank("ihCode")){
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collection.setCode(ihCode); |
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collection.setCodeStandard("Index Herbariorum");
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} |
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collection.setTownOrLocation(town); |
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collection.addSource(String.valueOf(collectionId), NAMESPACE_COLLECTION, sourceRef, null); |
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collectionsToSave.add(collection); //or subcollection ? |
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//subcollection |
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if (isNotBlank(subCollectionStr)){
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Collection subCollection = Collection.NewInstance(); |
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subCollection.setName(subCollectionStr); |
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subCollection.setSuperCollection(collection); |
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collectionsToSave.add(subCollection); //or subcollection ? |
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collection.addSource(String.valueOf(collectionId), NAMESPACE_SUBCOLLECTION, sourceRef, null); |
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} |
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} catch (Exception e) {
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logger.warn("Exception in collection: CollectionId " + collectionId + ". " + e.getMessage());
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// e.printStackTrace(); |
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} |
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} |
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logger.warn(pluralString + " to save: " + collectionsToSave.size()); |
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getCollectionService().save(collectionsToSave); |
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return success; |
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false; |
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} |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
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*/ |
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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//no related objects are needed |
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
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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#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected boolean doCheck(BerlinModelImportState state){
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IOValidator<BerlinModelImportState> validator = new AlgaTerraCollectionImportValidator(); |
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return validator.validate(state); |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName() |
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*/ |
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@Override |
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protected String getTableName() {
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return dbTableName; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString() |
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*/ |
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@Override |
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public String getPluralString() {
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return pluralString; |
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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.IImportConfigurator) |
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*/ |
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protected boolean isIgnore(BerlinModelImportState bmState){
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AlgaTerraImportState state = (AlgaTerraImportState)bmState; |
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return ! ( state.getAlgaTerraConfigurator().isDoSpecimen() || state.getAlgaTerraConfigurator().isDoTypes() ); |
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} |
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} |
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| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraImportConfigurator.java | ||
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| 64 | 64 |
, BerlinModelWebMarkerCategoryImport.class |
| 65 | 65 |
, BerlinModelWebMarkerImport.class |
| 66 | 66 |
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, AlgaTerraCollectionImport.class |
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| 67 | 68 |
, AlgaTerraSpecimenImport.class |
| 68 | 69 |
, AlgaTerraTypeImport.class |
| 69 | 70 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImport.java | ||
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| 50 | 50 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.occurrence.Collection; |
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| 53 | 54 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 54 | 55 |
import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
| 55 | 56 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 157 | 158 |
DerivedUnitFacade facade = getDerivedUnit(state, ecoFactId, ecoFactMap, type); |
| 158 | 159 |
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//field observation |
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handleSingleSpecimen(rs, facade, state); |
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handleSingleSpecimen(rs, facade, state, partitioner);
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| 161 | 162 |
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| 162 | 163 |
handleEcoFactSpecificSpecimen(rs,facade, state); |
| 163 | 164 |
|
| ... | ... | |
| 465 | 466 |
Set<String> taxonIdSet = new HashSet<String>(); |
| 466 | 467 |
Set<String> fieldObservationIdSet = new HashSet<String>(); |
| 467 | 468 |
Set<String> termsIdSet = new HashSet<String>(); |
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Set<String> collectionIdSet = new HashSet<String>(); |
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| 468 | 470 |
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| 469 | 471 |
while (rs.next()){
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| 470 | 472 |
handleForeignKey(rs, taxonIdSet, "taxonId"); |
| ... | ... | |
| 472 | 474 |
handleForeignKey(rs, termsIdSet, "ClimateFk"); |
| 473 | 475 |
handleForeignKey(rs, termsIdSet, "HabitatFk"); |
| 474 | 476 |
handleForeignKey(rs, termsIdSet, "LifeFormFk"); |
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handleForeignKey(rs, collectionIdSet, "CollectionFk"); |
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| 475 | 478 |
} |
| 476 | 479 |
|
| 477 | 480 |
//taxon map |
| ... | ... | |
| 488 | 491 |
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
| 489 | 492 |
result.put(nameSpace, fieldObservationMap); |
| 490 | 493 |
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//collections |
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nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION; |
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cdmClass = Collection.class; |
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idSet = collectionIdSet; |
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Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
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result.put(nameSpace, collectionMap); |
|
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|
|
| 501 |
//sub-collections |
|
| 502 |
nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION; |
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cdmClass = Collection.class; |
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idSet = collectionIdSet; |
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Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 506 |
result.put(nameSpace, subCollectionMap); |
|
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|
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| 491 | 508 |
//terms |
| 492 | 509 |
nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE; |
| 493 | 510 |
cdmClass = FieldObservation.class; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImportBase.java | ||
|---|---|---|
| 13 | 13 |
import java.sql.Date; |
| 14 | 14 |
import java.sql.ResultSet; |
| 15 | 15 |
import java.sql.SQLException; |
| 16 |
import java.util.Map; |
|
| 16 | 17 |
import java.util.Set; |
| 17 | 18 |
import java.util.UUID; |
| 18 | 19 |
|
| ... | ... | |
| 22 | 23 |
|
| 23 | 24 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 24 | 25 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase; |
| 26 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport; |
|
| 27 |
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
|
| 25 | 28 |
import eu.etaxonomy.cdm.io.common.Source; |
| 26 | 29 |
import eu.etaxonomy.cdm.model.agent.Team; |
| 27 | 30 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
| ... | ... | |
| 35 | 38 |
import eu.etaxonomy.cdm.model.location.ReferenceSystem; |
| 36 | 39 |
import eu.etaxonomy.cdm.model.location.TdwgArea; |
| 37 | 40 |
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry; |
| 41 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 42 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
|
| 38 | 43 |
|
| 39 | 44 |
/** |
| 40 | 45 |
* @author a.mueller |
| ... | ... | |
| 148 | 153 |
return "Locality"; |
| 149 | 154 |
} |
| 150 | 155 |
|
| 151 |
protected void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
|
|
| 156 |
protected void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {
|
|
| 152 | 157 |
//FIXME missing fields #3084, #3085, #3080 |
| 153 | 158 |
try {
|
| 154 | 159 |
|
| ... | ... | |
| 167 | 172 |
String collectorsNumber = rs.getString("CollectorsNumber");
|
| 168 | 173 |
Date collectionDateStart = rs.getDate("CollectionDate");
|
| 169 | 174 |
Date collectionDateEnd = rs.getDate("CollectionDateEnd");
|
| 170 |
|
|
| 175 |
|
|
| 176 |
Integer collectionFk = nullSafeInt(rs,"CollectionFk"); |
|
| 177 |
|
|
| 178 |
|
|
| 171 | 179 |
//location |
| 172 | 180 |
facade.setLocality(locality); |
| 173 | 181 |
|
| ... | ... | |
| 204 | 212 |
facade.setDistanceToWaterSurface(intDepth); |
| 205 | 213 |
} |
| 206 | 214 |
} |
| 207 |
|
|
| 208 | 215 |
|
| 209 | 216 |
//field |
| 210 | 217 |
facade.setFieldNumber(collectorsNumber); |
| ... | ... | |
| 215 | 222 |
//areas |
| 216 | 223 |
makeAreas(state, rs, facade); |
| 217 | 224 |
|
| 225 |
//collection |
|
| 226 |
if (collectionFk != null){
|
|
| 227 |
Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class); |
|
| 228 |
if (subCollection != null){
|
|
| 229 |
facade.setCollection(subCollection); |
|
| 230 |
}else{
|
|
| 231 |
Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class); |
|
| 232 |
facade.setCollection(collection); |
|
| 233 |
} |
|
| 234 |
} |
|
| 218 | 235 |
|
| 219 | 236 |
//notes |
| 220 | 237 |
//TODO is this an annotation on field observation or on the derived unit? |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraTypeImport.java | ||
|---|---|---|
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 39 |
import eu.etaxonomy.cdm.model.occurrence.Collection; |
|
| 39 | 40 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
| 40 | 41 |
import eu.etaxonomy.cdm.model.occurrence.FieldObservation; |
| 41 | 42 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 151 | 152 |
DerivedUnitFacade facade = getDerivedUnit(state, typeSpecimenId, typeSpecimenMap, type, ecoFactMap, ecoFactId); |
| 152 | 153 |
|
| 153 | 154 |
//field observation |
| 154 |
handleSingleSpecimen(rs, facade, state); |
|
| 155 |
handleSingleSpecimen(rs, facade, state, partitioner);
|
|
| 155 | 156 |
|
| 156 | 157 |
handleTypeSpecimenSpecificSpecimen(rs,facade, state); |
| 157 | 158 |
|
| ... | ... | |
| 314 | 315 |
Set<String> ecoFieldObservationIdSet = new HashSet<String>(); |
| 315 | 316 |
Set<String> typeSpecimenIdSet = new HashSet<String>(); |
| 316 | 317 |
Set<String> termsIdSet = new HashSet<String>(); |
| 318 |
Set<String> collectionIdSet = new HashSet<String>(); |
|
| 317 | 319 |
|
| 318 | 320 |
while (rs.next()){
|
| 319 | 321 |
handleForeignKey(rs, nameIdSet, "nameFk"); |
| 320 | 322 |
handleForeignKey(rs, ecoFieldObservationIdSet, "ecoFactFk"); |
| 321 | 323 |
handleForeignKey(rs, typeSpecimenIdSet, "TypeSpecimenId"); |
| 324 |
handleForeignKey(rs, collectionIdSet, "CollectionFk"); |
|
| 322 | 325 |
} |
| 323 | 326 |
|
| 324 | 327 |
//name map |
| ... | ... | |
| 342 | 345 |
Map<String, FieldObservation> typeSpecimenMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
| 343 | 346 |
result.put(nameSpace, typeSpecimenMap); |
| 344 | 347 |
|
| 348 |
|
|
| 349 |
//collections |
|
| 350 |
nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION; |
|
| 351 |
cdmClass = Collection.class; |
|
| 352 |
idSet = collectionIdSet; |
|
| 353 |
Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 354 |
result.put(nameSpace, collectionMap); |
|
| 355 |
|
|
| 356 |
//sub-collections |
|
| 357 |
nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION; |
|
| 358 |
cdmClass = Collection.class; |
|
| 359 |
idSet = collectionIdSet; |
|
| 360 |
Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 361 |
result.put(nameSpace, subCollectionMap); |
|
| 362 |
|
|
| 345 | 363 |
|
| 346 | 364 |
// |
| 347 | 365 |
// //terms |
Also available in: Unified diff
adding collections to AlgaTerra import