-// $Id$\r
/**\r
* Copyright (C) 2009 EDIT\r
* European Distributed Institute of Taxonomy\r
\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.apache.lucene.queryParser.ParseException;\r
import org.hibernate.search.spatial.impl.Rectangle;\r
+import org.springframework.transaction.annotation.Transactional;\r
\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;\r
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;\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.FieldUnitDTO;\r
import eu.etaxonomy.cdm.api.service.dto.PreservedSpecimenDTO;\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.api.service.util.TaxonRelationshipEdge;\r
-import eu.etaxonomy.cdm.model.common.ICdmBase;\r
import eu.etaxonomy.cdm.model.common.Language;\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.description.TaxonDescription;\r
import eu.etaxonomy.cdm.model.location.Country;\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.TaxonNameBase;\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.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.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
\r
/**\r
* @author a.babadshanjan\r
- * @created 01.09.2008\r
+ * @since 01.09.2008\r
*/\r
public interface IOccurrenceService extends IIdentifiableEntityService<SpecimenOrObservationBase> {\r
\r
* properties to be initialized\r
* @return\r
*/\r
- public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonNameBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
/**\r
* Returns a List of Media that are associated with a given occurence\r
* @param taxonbase the taxon concept associated with these determinations (can be null for all taxon concepts)\r
* @return a count of determination events\r
*/\r
- public int countDeterminations(SpecimenOrObservationBase occurence,TaxonBase taxonbase);\r
+ public long countDeterminations(SpecimenOrObservationBase occurence,TaxonBase taxonbase);\r
\r
/**\r
* Returns a List of determinations that have been made for a given occurence\r
* {@link DerivedUnit}s found in the data base.\r
* @return a list of {@link UuidAndTitleCache}\r
*/\r
- public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache();\r
+ public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern);\r
\r
public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException;\r
\r
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,\r
Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
+ /**\r
+ * The method will search for specimen associated with the taxon nodes.<br>\r
+ * It will search for 3 possible association types: <br>\r
+ * - via IndividualAssociations of the taxon<br>\r
+ * - via TypeDesignations of the taxon name<br>\r
+ * - via Determinations of the taxon or taxon name<br>\r
+ * <br>\r
+ * more are covered in\r
+ * {@link IOccurrenceService#findByTitle(IIdentifiableEntityServiceConfigurator)}\r
+ * @param taxonNodeUuids\r
+ * a list of {@link UUID}s of the taxon nodes\r
+ * @param limit\r
+ * @param start\r
+ * @return a collection of {@link SpecimenNodeWrapper} containing the\r
+ * {@link TaxonNode} and the corresponding {@link UuidAndTitleCache}\r
+ * object for the specimen found for this taxon node\r
+ */\r
+ public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start);\r
+\r
+\r
/**\r
* Lists all instances of {@link FieldUnit} which are\r
* associated <b>directly or indirectly</b>with the <code>taxon</code> specified\r
/**\r
* Retrieves all {@link FieldUnit}s for the {@link SpecimenOrObservationBase} with the given {@link UUID}.<br>\r
* @param specimenUuid the UUID of the specimen\r
+ * @param propertyPaths the property path\r
* @return either a collection of FieldUnits this specimen was derived from, the FieldUnit itself\r
* if this was a FieldUnit or an empty collection if no FieldUnits were found\r
*/\r
- public Collection<FieldUnit> getFieldUnits(UUID specimenUuid);\r
+ public Collection<FieldUnit> findFieldUnits(UUID specimenUuid, List<String> propertyPaths);\r
\r
/**\r
* @param clazz\r
* @throws ParseException\r
*/\r
Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(Class<? extends SpecimenOrObservationBase> clazz,\r
- String queryString, Rectangle boundingBox, List<Language> languages, boolean highlightFragments, Integer pageSize,\r
- Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException,\r
- IOException, ParseException;\r
+ String queryString, Rectangle boundingBox, List<Language> languages, boolean highlightFragments,\r
+ Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths)\r
+ throws IOException, LuceneParseException;\r
/**\r
* See {@link #listByAssociatedTaxon(Class, Set, String, Integer, Integer, Integer, List, List)}\r
*\r
public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate);\r
\r
/**\r
- * Assembles a {@link FieldUnitDTO} for the given field unit uuid which is associated to the {@link Taxon}.<br>\r
- * <br>\r
- * For the meaning of "associated" see also {@link #listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List)}\r
+ * Assembles a {@link FieldUnitDTO} for the given field unit.<br>\r
+ *\r
* @param fieldUnit\r
- * @param associatedTaxonUuid\r
* @return a DTO with all the assembled information\r
*/\r
- public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit, UUID associatedTaxonUuid);\r
+ public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit);\r
\r
/**\r
* Assembles a {@link PreservedSpecimenDTO} for the given derived unit.\r
*/\r
public PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit);\r
\r
- /**\r
- * Returns a collection of {@link ICdmBase}s that are not persisted via cascading when saving the given specimen (mostly DefinedTerms).\r
- * @param specimen the specimen that is checked for non-cascaded elements.\r
- * @return collection of non-cascaded element associated with the specimen\r
- */\r
- public Collection<ICdmBase> getNonCascadedAssociatedElements(SpecimenOrObservationBase<?> specimen);\r
-\r
/**\r
* Deletes the specified specimen according to the setting in the {@link SpecimenDeleteConfigurator}.<br>\r
* @param specimen the specimen which shoul be deleted\r
*/\r
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
+\r
/**\r
- * Retrieves all associated taxa for the given specimen\r
+ * Retrieves all taxa linked via {@link IndividualsAssociation} with the given specimen.<br>\r
+ * @param specimen the specimen which is linked to the taxa\r
+ * @param limit\r
+ * @param start\r
+ * @param orderHints\r
+ * @param propertyPaths\r
+ * @return a collection of associated taxa\r
+ */\r
+ public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ /**\r
+ * @see #listIndividualsAssociationTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)\r
+ */\r
+ public Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+\r
+ /**\r
+ * Retrieves all associated taxa for the given specimen (via type designations, determination, individuals associations)\r
* @param specimen\r
* @param limit\r
* @param start\r
* @param propertyPaths\r
* @return\r
*/\r
- public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ /**\r
+ * @see #listAssociatedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)axa\r
+ */\r
+ public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+\r
+ /**\r
+ * Retrieves all taxa that the given specimen is determined as\r
+ * @param specimen\r
+ * @param limit\r
+ * @param start\r
+ * @param orderHints\r
+ * @param propertyPaths\r
+ * @return collection of all taxa the given specimen is determined as\r
+ */\r
+ public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ /**\r
+ * @see #listDeterminedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)\r
+ */\r
+ public Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
/**\r
* Retrieves all {@link DeterminationEvent}s which have the given specimen set as identified unit.\r
- * @param specimen the type specimen\r
+ * @param specimen\r
* @param limit\r
* @param start\r
* @param orderHints\r
* @param propertyPaths\r
- * @return collection of all designations with the given type specimen\r
+ * @return collection of all determination events with the given specimen\r
*/\r
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
+ /**\r
+ * Retrieves all taxa with a {@link SpecimenTypeDesignation} with the given specimen as a type specimen.\r
+ * @param specimen the type specimen\r
+ * @param specimen\r
+ * @param limit\r
+ * @param start\r
+ * @param orderHints\r
+ * @param propertyPaths\r
+ * @return a collection of all taxa where the given specimen is the type specimen\r
+ */\r
+ public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ /**\r
+ * @see #listTypeDesignationTaxa(DerivedUnit, Integer, Integer, List, List)a\r
+ */\r
+ public Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, boolean includeUnpublished,\r
+ Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+\r
+ /**\r
+ * Retrieves all {@link SpecimenTypeDesignation}s which have the given specimens as a type specimen.\r
+ * @param specimens the type specimens\r
+ * @param limit\r
+ * @param start\r
+ * @param orderHints\r
+ * @param propertyPaths\r
+ * @return map of all designations with the given type specimens\r
+ */\r
+ public Map<DerivedUnit, Collection<SpecimenTypeDesignation>> listTypeDesignations(Collection<DerivedUnit> specimens, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+\r
/**\r
* Retrieves all {@link SpecimenTypeDesignation}s which have the given specimen as a type specimen.\r
* @param specimen the type specimen\r
* @param propertyPaths\r
* @return collection of all designations with the given type specimen\r
*/\r
- public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
+ public Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
/**\r
* Retrieves all {@link DescriptionBase}s that have the given specimen set as described specimen.\r
\r
/**\r
* Returns the number of specimens that match the given parameters\r
+ * <br>\r
+ * <b>NOTE - issue #6484:</b> the parameters {@link FindOccurrencesConfigurator#getAssignmentStatus()}\r
+ * and {@link FindOccurrencesConfigurator#isRetrieveIndirectlyAssociatedSpecimens()} are not evaluated\r
+ * in the count method\r
* @param clazz the class to match\r
* @param queryString the queryString to match\r
* @param type the {@link SpecimenOrObservationType} to match\r
* authorTeam.persistentTitleCache\r
* @return the number of found specimens\r
*/\r
- public int countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config);\r
+ public long countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config);\r
\r
/**\r
* Return the all {@link SpecimenOrObservationBase}s of the complete\r
*/\r
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen);\r
\r
+ /**\r
+ * Returns all child derivatives of the given specimen.\r
+ * @param specimen the UUID of a specimen or observation\r
+ * @return an unordered list of all child derivatives\r
+ */\r
+ public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid);\r
+\r
+ /**\r
+ * Returns all {@link FieldUnit}s that are referencing this {@link GatheringEvent}\r
+ * @param gatheringEventUuid the {@link UUID} of the gathering event\r
+ * @return a list of field units referencing the gathering event\r
+ */\r
+ public List<FieldUnit> findFieldUnitsForGatheringEvent(UUID gatheringEventUuid);\r
+\r
+\r
+ /**\r
+ * Returns a list of {@link UuidAndTitleCache} for the specimens found with the\r
+ * given configurator\r
+ * @param config the configurator for the search\r
+ * @return a list of UuidAndTitleCache object\r
+ */\r
+ @Transactional(readOnly = true)\r
+ public Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(\r
+ FindOccurrencesConfigurator config);\r
+\r
+ /**\r
+ * Returns a list of {@link PreservedSpecimenDTO} 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
+ */\r
+ @Transactional(readOnly = true)\r
+ public List<PreservedSpecimenDTO> findByTitlePreservedSpecimenDTO(\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
+ */\r
+\r
+ FieldUnitDTO findFieldUnitDTO(DerivateDTO derivedUnitDTO, Collection<FieldUnitDTO> fieldUnits, HashMap<UUID, DerivateDTO> alreadyCollectedSpecimen);\r
+\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
+ * @param derivedUnitUuid\r
+ * @return\r
+ */\r
+ FieldUnitDTO loadFieldUnitDTO(UUID derivedUnitUuid);\r
+\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff