-// $Id$\r
/**\r
* Copyright (C) 2009 EDIT\r
* European Distributed Institute of Taxonomy\r
import java.io.IOException;\r
import java.util.Collection;\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.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.CdmBase;\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.TaxonDescription;\r
import eu.etaxonomy.cdm.model.location.Country;\r
import eu.etaxonomy.cdm.model.media.Media;\r
-import eu.etaxonomy.cdm.model.molecular.AmplificationResult;\r
import eu.etaxonomy.cdm.model.molecular.DnaSample;\r
import eu.etaxonomy.cdm.model.molecular.Sequence;\r
-import eu.etaxonomy.cdm.model.molecular.SingleRead;\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
\r
/**\r
* Returns a paged list of occurrences that have been determined to belong\r
* to the taxon concept determinedAs, optionally restricted to objects\r
- * belonging to a class that that extends SpecimenOrObservationBase.\r
+ * belonging to a class that that extends SpecimenOrObservationBase. This\r
+ * will also consider specimens that are determined as a taxon concept\r
+ * belonging to the synonymy of the given taxon concept.\r
* <p>\r
* In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this\r
* method only takes SpecimenOrObservationBase instances into account which\r
*/\r
public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
+ /**\r
+ * Returns a paged list of occurrences that have been determined to belong\r
+ * to the taxon name determinedAs, optionally restricted to objects\r
+ * belonging to a class that that extends SpecimenOrObservationBase.\r
+ * <p>\r
+ * In contrast to {@link #listByAnyAssociation(Class, Taxon, List)} this\r
+ * method only takes SpecimenOrObservationBase instances into account which\r
+ * are actually determined as the taxon specified by\r
+ * <code>determinedAs</code>.\r
+ *\r
+ * @param type\r
+ * The type of entities to return (can be null to count all\r
+ * entities of type <T>)\r
+ * @param determinedAs\r
+ * the taxon name that the occurrences have been determined to\r
+ * belong to\r
+ * @param pageSize\r
+ * The maximum number of objects returned (can be null for all\r
+ * matching objects)\r
+ * @param pageNumber\r
+ * The offset (in pageSize chunks) from the start of the result\r
+ * set (0 - based, can be null, equivalent of starting at the\r
+ * beginning of the recordset)\r
+ * @param orderHints\r
+ * Supports path like <code>orderHints.propertyNames</code> which\r
+ * include *-to-one properties like createdBy.username or\r
+ * authorTeam.persistentTitleCache\r
+ * @param propertyPaths\r
+ * properties to be initialized\r
+ * @return\r
+ */\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
*\r
*/\r
public Pager<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);\r
\r
+ /**\r
+ * Returns all media attached to this occurence and its children. Also takes\r
+ * {@link MediaSpecimen} and molecular images into account.\r
+ *\r
+ * @param occurence the occurence and its children from which the media to get\r
+ * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)\r
+ * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}\r
+ * @return a Pager of media instances\r
+ */\r
+ public Pager<Media> getMediainHierarchy(SpecimenOrObservationBase rootOccurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths);\r
+\r
/**\r
* Returns a count of determinations that have been made for a given occurence and for a given taxon concept\r
*\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
+ * @param orderHints\r
+ * @return a list 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 List<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,\r
+ Integer limit, Integer start, List<OrderHint> orderHints);\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> getFieldUnits(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
*/\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
public DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config);\r
\r
/**\r
- * Deletes the specified specimen and all sub derivates.<br>\r
- * <b>Note:</b> Be sure to allow child deletion in the config.\r
- * @param from the specimen which should be deleted with all its sub derivates\r
- * @param config the {@link SpecimenDeleteConfigurator} to specify how the deletion should be handled\r
- * @return the {@link DeleteResult} which holds information about the outcome of this operation\r
- */\r
- public DeleteResult deleteDerivateHierarchy(CdmBase from, SpecimenDeleteConfigurator config);\r
-\r
- /**\r
- * Deletes the specified specimen and all sub derivates by first loading the corresponding uuids\r
- * and then calling {@link #deleteDerivateHierarchy(CdmBase, SpecimenDeleteConfigurator) deleteDerivateHierarchy}\r
- * @param fromUuid uuid of the specimen which should be deleted with all its sub derivates\r
- * @param config the {@link SpecimenDeleteConfigurator} to specify how the deletion should be handled\r
- * @return {@link DeleteResult} which holds information about the outcome of this operation\r
+ * Deletes the specified specimen belonging to the given {@link UUID}\r
+ * according to the setting in the {@link SpecimenDeleteConfigurator}.\r
+ *\r
+ * @param specimen\r
+ * the specimen which shoul be deleted\r
+ * @param config\r
+ * specifies options if and how the specimen should be deleted\r
+ * like e.g. including all of its children\r
+ * @return the {@link DeleteResult} which holds information about the\r
+ * outcome of this operation\r
*/\r
- public DeleteResult deleteDerivateHierarchy(UUID fromUuid, SpecimenDeleteConfigurator config);\r
+ public DeleteResult delete(UUID specimenUuid, SpecimenDeleteConfigurator config);\r
\r
/**\r
* Retrieves all {@link IndividualsAssociation} with the given specimen.<br>\r
*/\r
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);\r
\r
+\r
+ /**\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, Integer limit,\r
+ 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 orderHints\r
+ * @param propertyPaths\r
+ * @return\r
+ */\r
+ public Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, 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, Integer limit, Integer start,\r
+ 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\r
+ * @param limit\r
+ * @param start\r
+ * @param orderHints\r
+ * @param propertyPaths\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, Integer limit,\r
+ 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
public List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen);\r
\r
/**\r
- * Deletes a {@link SingleRead} from the given {@link Sequence} and its {@link AmplificationResult}.\r
- * @param singleRead the single read to delete\r
- * @param sequence the sequence to which the single read belongs\r
- * @return the {@link DeleteResult} which holds information about the outcome of this operation\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 DeleteResult deleteSingleRead(SingleRead singleRead, Sequence sequence);\r
+ public List<DerivedUnit> getAllChildDerivatives(UUID specimenUuid);\r
\r
/**\r
- * Deletes a {@link SingleRead} from the given {@link Sequence} and its {@link AmplificationResult},\r
- * by first loading the corresponding uuids and then calling {@link #deleteSingleRead(SingleRead, Sequence) deleteSingleRead}\r
- * @param singleReadUuid uuid of the single read to delete\r
- * @param sequenceUuid uuid of the sequence to which the single read belongs\r
- * @return the {@link DeleteResult} which holds information about the outcome of this operation\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> getFieldUnitsForGatheringEvent(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
- public DeleteResult deleteSingleRead(UUID singleReadUuid, UUID sequenceUuid);\r
+ @Transactional(readOnly = true)\r
+ public Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(\r
+ FindOccurrencesConfigurator config);\r
\r
}\r
BGBM BDI Projects / cdmlib.git / blobdiff