\r
import java.io.IOException;\r
import java.util.Collection;\r
-import java.util.HashMap;\r
import java.util.List;\r
import java.util.Map;\r
import java.util.Set;\r
import java.util.UUID;\r
\r
+import org.apache.lucene.index.CorruptIndexException;\r
import org.hibernate.search.spatial.impl.Rectangle;\r
import org.springframework.transaction.annotation.Transactional;\r
\r
import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;\r
import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;\r
import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;\r
-import eu.etaxonomy.cdm.api.service.dto.DerivateDTO;\r
+import eu.etaxonomy.cdm.api.service.dto.DerivedUnitDTO;\r
import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;\r
-import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;\r
+import eu.etaxonomy.cdm.api.service.dto.SpecimenOrObservationBaseDTO;\r
import eu.etaxonomy.cdm.api.service.pager.Pager;\r
import eu.etaxonomy.cdm.api.service.search.LuceneParseException;\r
import eu.etaxonomy.cdm.api.service.search.SearchResult;\r
import eu.etaxonomy.cdm.model.description.DescriptionBase;\r
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;\r
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;\r
-import eu.etaxonomy.cdm.model.location.Country;\r
+import eu.etaxonomy.cdm.model.description.TaxonDescription;\r
import eu.etaxonomy.cdm.model.location.Point;\r
import eu.etaxonomy.cdm.model.media.Media;\r
import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
import eu.etaxonomy.cdm.model.molecular.Sequence;\r
+import eu.etaxonomy.cdm.model.name.HomotypicalGroup;\r
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;\r
import eu.etaxonomy.cdm.model.name.TaxonName;\r
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;\r
import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;\r
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;\r
+import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;\r
+import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;\r
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;\r
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;\r
import eu.etaxonomy.cdm.model.taxon.Taxon;\r
import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
+import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;\r
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;\r
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;\r
import eu.etaxonomy.cdm.persistence.query.OrderHint;\r
* @author a.babadshanjan\r
* @since 01.09.2008\r
*/\r
-public interface IOccurrenceService extends IIdentifiableEntityService<SpecimenOrObservationBase> {\r
-\r
- public Country getCountryByIso(String iso639);\r
-\r
- public List<Country> getCountryByName(String name);\r
+public interface IOccurrenceService\r
+ extends IIdentifiableEntityService<SpecimenOrObservationBase> {\r
\r
/**\r
* Returns a paged list of occurrences that have been determined to belong\r
\r
\r
/**\r
- * Lists all instances of {@link FieldUnit} which are\r
+ * Lists all root units which are\r
* associated <b>directly or indirectly</b>with the <code>taxon</code> specified\r
* as parameter. "Indirectly" means that a sub derivate of the FieldUnit is\r
* directly associated with the given taxon.\r
*\r
* @param <T>\r
* @param type\r
+ * Restriction to a specific subtype, may be null.\r
* @param associatedTaxon\r
* @param Set<TaxonRelationshipVector> includeRelationships. TaxonRelationships will not be taken into account if this is <code>NULL</code>.\r
* @param maxDepth TODO\r
* @param propertyPaths\r
* @return\r
*/\r
- public Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ public <T extends SpecimenOrObservationBase> Collection<T> listRootUnitsByAssociatedTaxon(Class<T> type, Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);\r
+\r
+\r
+ /**\r
+ * @deprecated replace by {@link #listRootUnitsByAssociatedTaxon(Class, Taxon, List, List)}\r
+ */\r
+ @Deprecated\r
+ public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
/**\r
* See {@link #listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List)}\r
*/\r
- public Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,\r
+ public <T extends SpecimenOrObservationBase> Pager<T> pageRootUnitsByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,\r
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
/**\r
* See {@link #listByAssociatedTaxon(Class, Set, Taxon, Integer, Integer, Integer, List, List)}\r
*\r
* @param type\r
+ * Restriction to subtype of <code>SpecimenOrObservationBase</code>, can be NULL.\r
* @param includeRelationships\r
* @param associatedTaxon\r
* @param maxDepth\r
*/\r
public Collection<FieldUnit> findFieldUnits(UUID specimenUuid, List<String> propertyPaths);\r
\r
+ /**\r
+ * Retrieves top most originals for a {@link SpecimenOrObservationBase} in the derivation graph by recursively\r
+ * walking all {@link DerivationEvent}s.\r
+ * In most cases item in the returned collection will be {@link FieldUnit FieldUnits} but also DerivedUnits are possible, in\r
+ * cases where no FieledUnit exists.\r
+ *\r
+ * @param specimenUuid the UUID of the specimen\r
+ * @param propertyPaths the property path\r
+ * @return either a collection of root units\r
+ */\r
+ public Collection<SpecimenOrObservationBase> findRootUnits(UUID specimenUuid, List<String> propertyPaths);\r
+\r
/**\r
* @param clazz\r
* @param queryString\r
public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit);\r
\r
/**\r
- * Assembles a {@link PreservedSpecimenDTO} for the given derived unit.\r
+ * Assembles a {@link DerivedUnitDTO} for the given derived unit.\r
* @param derivedUnit\r
* @return a DTO with all the assembled information\r
*/\r
- public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit);\r
+ public DerivedUnitDTO assembleDerivedUnitDTO(DerivedUnit derivedUnit);\r
\r
/**\r
* Deletes the specified specimen according to the setting in the {@link SpecimenDeleteConfigurator}.<br>\r
*/\r
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
- /**\r
- * Gets all description elements that are used for describing the character\r
- * states of the given specimen\r
- *\r
- * @param specimen\r
- * the specimen for which the character state description\r
- * elements should be retrieved\r
- * @return a collection of all character state description elements for this\r
- * specimen\r
- */\r
- public Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen);\r
-\r
/**\r
* Gets all description elements that are used for describing the character\r
* states of the given specimen\r
* Returns the most significant identifier for the given {@link DerivedUnit}.\r
* @param derivedUnit the derived unit to check\r
* @return the identifier string\r
+ * @deprecated use {@link DerivedUnit#getMostSignificantIdentifier()} instead\r
*/\r
+ @Deprecated\r
public String getMostSignificantIdentifier(DerivedUnit derivedUnit);\r
\r
/**\r
FindOccurrencesConfigurator config);\r
\r
/**\r
- * Returns a list of {@link PreservedSpecimenDTO} for the specimens found with the\r
+ * Returns a list of {@link DerivedUnitDTO} for the specimens found with the\r
* given configurator\r
* @param config the configurator for the search\r
- * @return a list of {@link PreservedSpecimenDTO} object\r
+ * @return a list of {@link DerivedUnitDTO} object\r
*/\r
@Transactional(readOnly = true)\r
- public List<PreservedSpecimenDTO> findByTitlePreservedSpecimenDTO(\r
+ public List<DerivedUnitDTO> findByTitleDerivedUnitDTO(\r
FindOccurrencesConfigurator config);\r
\r
- /**\r
- * @param queryString\r
- * @param propertyPaths\r
- * @return\r
- * @throws IOException\r
- */\r
- FieldUnitDTO findByAccessionNumber(\r
- String accessionNumberString, List<OrderHint> orderHints,\r
- List<String> propertyPaths);\r
-\r
- /**\r
- * @param includedRelationships\r
- * @param associatedTaxon\r
- * @param maxDepth\r
- * @param pageSize\r
- * @param pageNumber\r
- * @param orderHints\r
- * @param propertyPaths\r
- * @return\r
- */\r
- List<FieldUnitDTO> findFieldUnitDTOByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,\r
- UUID associatedTaxonUuid);\r
\r
/**\r
- * @param derivedUnitUuid\r
- * @param propertyPaths\r
- * @return\r
+ * Collects the <code>FieldUnits</code> which are at the root of the derivation event\r
+ * graph in which the {@link DerivedUnit} with the specified <code>findByAccessionNumber</code>\r
+ * is found.\r
*/\r
+ SpecimenOrObservationBaseDTO findByAccessionNumber(String accessionNumberString, List<OrderHint> orderHints);\r
\r
- FieldUnitDTO findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen);\r
\r
+ List<SpecimenOrObservationBaseDTO> listRootUnitDTOsByAssociatedTaxon(Set<TaxonRelationshipEdge> includedRelationships,\r
+ UUID associatedTaxonUuid, List<String> propertyPaths);\r
\r
- /**\r
- * @param fieldUnitUuids\r
- * @return\r
- */\r
public List<Point> findPointsForFieldUnitList(List<UUID> fieldUnitUuids);\r
\r
/**\r
* Load the FieldUnitDTO for the given <code>derivedUnitUuid</code> with all intermediate derivatives and {@link eu.etaxonomy.cdm.api.service.dto.GatheringEventDTO}\r
+\r
* @param derivedUnitUuid\r
* @return\r
*/\r
BGBM BDI Projects / cdmlib.git / blobdiff