public interface IDescriptiveDataSetService extends IIdentifiableEntityService<DescriptiveDataSet>
Modifier and Type | Method and Description |
---|---|
UpdateResult |
addRowWrapperToDataset(java.util.Collection<SpecimenNodeWrapper> wrapper,
java.util.UUID datasetUuid)
Creates a
SpecimenRowWrapperDTO from the given SpecimenNodeWrapper.This service method is used when adding new specimen to the character matrix resp. |
SpecimenRowWrapperDTO |
createSpecimenRowWrapper(SpecimenDescription description,
java.util.UUID descriptiveDataSetUuid)
Creates a specimen row wrapper object for the given description
|
TaxonRowWrapperDTO |
createTaxonDescription(java.util.UUID dataSetUuid,
java.util.UUID taxonNodeUuid,
DescriptionType descriptionType)
Creates a new taxon description with the features defined in the dataset for the
taxon associated with the given taxon node.
|
TaxonRowWrapperDTO |
createTaxonRowWrapper(java.util.UUID taxonDescriptionUuid,
java.util.UUID descriptiveDataSetUuid)
Creates a taxon row wrapper object for the given description
|
TaxonDescription |
findDefaultDescription(java.util.UUID specimenDescriptionUuid,
java.util.UUID dataSetUuid)
Returns the first
TaxonDescription with DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION
found in the taxon node hierarchy of the associated taxon |
java.util.List<java.util.UUID> |
findFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet)
Lists all taxon nodes that match the filter set defined in the
DescriptiveDataSet given. |
SpecimenDescription |
findSpecimenDescription(java.util.UUID descriptiveDataSetUuid,
java.util.UUID specimenUuid,
boolean addDatasetSource)
Returns a
SpecimenDescription for a given specimen with corresponding
features according to the DescriptiveDataSet .If a description is found that matches all features of the data set this description will be returned. |
TaxonDescription |
findTaxonDescriptionByDescriptionType(java.util.UUID dataSetUuid,
java.util.UUID taxonNodeUuid,
DescriptionType descriptionType)
Returns a
TaxonDescription for a given taxon node with corresponding
features according to the DescriptiveDataSet and the having the given DescriptionType . |
UpdateResult |
generatePolytomousKey(java.util.UUID descriptiveDataSetUuid,
java.util.UUID taxonUuid)
Generates a
PolytomousKey for the given DescriptiveDataSet and sets
the given taxon as the taxonomic scope |
java.util.Map<DescriptionBase,java.util.Set<DescriptionElementBase>> |
getDescriptionElements(DescriptiveDataSet descriptiveDataSet,
java.util.Set<Feature> features,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a Map of descriptions each with the description elements that match
the supplied features (or all description elements if no features are supplied)
|
java.util.List<UuidAndTitleCache<DescriptiveDataSet>> |
getDescriptiveDataSetUuidAndTitleCache(java.lang.Integer limitOfInitialElements,
java.lang.String pattern)
Returns a list of
UuidAndTitleCache elements for all DescriptiveDataSet s in the data base |
java.util.ArrayList<RowWrapperDTO> |
getRowWrapper(java.util.UUID descriptiveDataSetUuid,
IProgressMonitor monitor)
Returns a collection of
RowWrapperDTO objects for the given DescriptiveDataSet .A RowWrapper represents on row in the character matrix. |
java.util.List<TermDto> |
getSupportedStatesForFeature(java.util.UUID featureUuid)
Returns all states for all supportedCategoricalEnumeration of this categorical feature
|
<T extends DescriptionElementBase> |
getTaxonFeatureDescriptionElementMap(java.lang.Class<T> clazz,
java.util.UUID descriptiveDataSetUuid,
DescriptiveSystemRole role) |
java.util.List<TaxonNode> |
loadFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet,
java.util.List<java.lang.String> propertyPaths)
Loads all taxon nodes that match the filter set defined in the
DescriptiveDataSet given. |
java.util.Collection<SpecimenNodeWrapper> |
loadSpecimens(DescriptiveDataSet descriptiveDataSet)
Loads all available specimens wrapped in a
SpecimenNodeWrapper object for
a given DescriptiveDataSet according to the filters set in the working set |
java.util.Collection<SpecimenNodeWrapper> |
loadSpecimens(java.util.UUID descriptiveDataSetUuid) |
DeleteResult |
removeDescription(java.util.UUID descriptionUuid,
java.util.UUID descriptiveDataSetUuid)
Removes the description specified by the given
UUID from the given DescriptiveDataSet . |
countByTitle, countByTitle, countByTitleWithRestrictions, deduplicate, find, findByIdentifier, findByMarker, findByTitle, findByTitle, findByTitleWithRestrictions, findTitleCache, findUuidAndTitleCacheByMarker, getRights, getSourcedObjectByIdInSource, getSources, getTitleCache, getUuidAndTitleCache, getUuidAndTitleCache, listByIdentifier, listByReferenceTitle, listByReferenceTitleWithRestrictions, listByTitle, listByTitleWithRestrictions, replace, search, updateCaches, updateCaches
countMarkers, getAnnotations, getMarkers, groupMarkers
getNextAuditEvent, getPreviousAuditEvent, isDeletable, pageAuditEvents, pageAuditEvents
clear, count, delete, delete, delete, exists, find, find, find, find, findById, findWithoutFlush, getSession, group, list, list, load, load, load, load, loadByIds, loadByIds, loadWithUpdate, lock, merge, merge, merge, merge, page, page, page, pageByParamWithRestrictions, refresh, refresh, save, save, saveOrUpdate, saveOrUpdate, update
java.util.Map<DescriptionBase,java.util.Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, java.util.Set<Feature> features, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
descriptiveDataSet
- the data set which the descriptions belong tofeatures
- restrict the returned description elements to those which have features in this setpageSize
- The maximum number of descriptions returned (can be null for all descriptions that belong to the data set)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based,
can be null, equivalent of starting at the beginning of the recordset). Descriptions are sorted by titleCachepropertyPaths
- properties to be initialized (applied to the descriptionElements)<T extends DescriptionElementBase> java.util.Map<UuidAndTitleCache,java.util.Map<java.util.UUID,java.util.Set<T>>> getTaxonFeatureDescriptionElementMap(java.lang.Class<T> clazz, java.util.UUID descriptiveDataSetUuid, DescriptiveSystemRole role)
java.util.List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(java.lang.Integer limitOfInitialElements, java.lang.String pattern)
UuidAndTitleCache
elements for all DescriptiveDataSet
s in the data baselimitOfInitialElements
- pattern
- java.util.ArrayList<RowWrapperDTO> getRowWrapper(java.util.UUID descriptiveDataSetUuid, IProgressMonitor monitor)
RowWrapperDTO
objects for the given DescriptiveDataSet
.descriptiveDataSetUuid
- the working set for which the row wrapper objects should be fetchedthe
- progress monitorjava.util.Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet)
SpecimenNodeWrapper
object for
a given DescriptiveDataSet
according to the filters set in the working setdescriptiveDataSet
- the data set for which the specimens should be fetchedjava.util.List<java.util.UUID> findFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet)
DescriptiveDataSet
given.the
- data set which defined the taxon node filterUUID
s from the filtered nodesUpdateResult addRowWrapperToDataset(java.util.Collection<SpecimenNodeWrapper> wrapper, java.util.UUID datasetUuid)
SpecimenRowWrapperDTO
from the given SpecimenNodeWrapper.DescriptiveDataSet
.wrapper
- the specimen wrapper to use for creating the row wrapperdatasetUuid
- the target datasetSpecimenRowWrapperDTO createSpecimenRowWrapper(SpecimenDescription description, java.util.UUID descriptiveDataSetUuid)
description
- the specimen description for which the wrapper should be createddescriptiveDataSetUuid
- the data set it should be used inTaxonDescription findTaxonDescriptionByDescriptionType(java.util.UUID dataSetUuid, java.util.UUID taxonNodeUuid, DescriptionType descriptionType)
TaxonDescription
for a given taxon node with corresponding
features according to the DescriptiveDataSet
and the having the given DescriptionType
.descriptiveDataSetUuid
- the uuid of the dataset defining the featurestaxonNodeUuid
- the uuid of the taxon node that links to the taxondescriptionType
- the DescriptionType
that the description should havenull
TaxonRowWrapperDTO createTaxonRowWrapper(java.util.UUID taxonDescriptionUuid, java.util.UUID descriptiveDataSetUuid)
taxonDescriptionUuid
- the taxon description for which the wrapper should be createddescriptiveDataSet
- the data set it should be used inSpecimenDescription findSpecimenDescription(java.util.UUID descriptiveDataSetUuid, java.util.UUID specimenUuid, boolean addDatasetSource)
SpecimenDescription
for a given specimen with corresponding
features according to the DescriptiveDataSet
.descriptiveDataSetUuid
- the uuid of the dataset defining the featuresspecimenUuid
- the uuid of the specimenaddDatasetSource
- if true
the source(s) of the descriptive dataset
will be added to the description if a new one is createdjava.util.List<TermDto> getSupportedStatesForFeature(java.util.UUID featureUuid)
featureUuid
- the feature which has to support categorical dataTaxonRowWrapperDTO createTaxonDescription(java.util.UUID dataSetUuid, java.util.UUID taxonNodeUuid, DescriptionType descriptionType)
descriptiveDataSetUuid
- the uuid of the dataset defining the featurestaxonNodeUuid
- the uuid of the taxon node that links to the taxondescriptionType
- the type of the descriptionDeleteResult removeDescription(java.util.UUID descriptionUuid, java.util.UUID descriptiveDataSetUuid)
UUID
from the given DescriptiveDataSet
.descriptionUuid
- the UUID of the description to deletedescriptiveDataSetUuid
- the UUID of the data set to deletejava.util.List<TaxonNode> loadFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet, java.util.List<java.lang.String> propertyPaths)
DescriptiveDataSet
given.the
- data set which defined the taxon node filterTaxonNode
s from the filtered nodesUpdateResult generatePolytomousKey(java.util.UUID descriptiveDataSetUuid, java.util.UUID taxonUuid)
PolytomousKey
for the given DescriptiveDataSet
and sets
the given taxon as the taxonomic scopedatasetUuid
- the data settaxonUuid
- the taxonomic scope of the keyTaxonDescription findDefaultDescription(java.util.UUID specimenDescriptionUuid, java.util.UUID dataSetUuid)
TaxonDescription
with DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION
found in the taxon node hierarchy of the associated taxonspecimenDescriptionUuid
- the specimen descriptiondataSetUuid
- the data setnull
java.util.Collection<SpecimenNodeWrapper> loadSpecimens(java.util.UUID descriptiveDataSetUuid)
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