Interface IScreeningApiServer
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- All Superinterfaces:
ch.systemsx.cisd.common.api.IRpcService
public interface IScreeningApiServer extends ch.systemsx.cisd.common.api.IRpcService
This interface is a part of the official public screening API. It is forbidden to change it in a non-backward-compatible manner without discussing it with all screening customers.
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
JSON_SERVICE_URL
static int
MAJOR_VERSION
The major version of this service.static java.lang.String
SERVICE_NAME
Name of this service for which it is registered at the RPC name server.static java.lang.String
SERVICE_URL
Service part of the URL to access this service remotely.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<IDatasetIdentifier>
getDatasetIdentifiers(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCodes)
Converts a given list of dataset codes to dataset identifiers.ExperimentImageMetadata
getExperimentImageMetadata(java.lang.String sessionToken, ExperimentIdentifier experimentIdentifer)
Returns aggregated metadata for all images/plates within one experiment.java.util.Map<java.lang.String,LogicalImageInfo>
getImageInfo(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCode)
Returns information about logical image in the given image datasets.java.util.Map<java.lang.String,java.util.List<ImageResolution>>
getImageResolutions(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCode)
Returns information about available image resolutions for the given image datasets.java.util.List<PlateMetadata>
getPlateMetadataList(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates)
Fetches the contents of a given list of plates.ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
getPlateSample(java.lang.String sessionToken, PlateIdentifier plateIdentifier)
For a given plateIdentifier, return the correspondingSample
.ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample
getWellSample(java.lang.String sessionToken, WellIdentifier wellIdentifier)
For a given wellIdentifier, return the correspondingSample
including properties.java.util.List<java.lang.String>
listAvailableFeatureCodes(java.lang.String sessionToken, java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableFeatureCodes(String, List)
method for each group of objects on appropriate data store server.java.util.List<FeatureInformation>
listAvailableFeatures(java.lang.String sessionToken, java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableFeatures(String, List)
method for each group of objects on appropriate data store server.java.util.List<DatasetImageRepresentationFormats>
listAvailableImageRepresentationFormats(java.lang.String sessionToken, java.util.List<? extends IDatasetIdentifier> imageDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableImageRepresentationFormats(String, List)
method for each group of objects on appropriate data store server.java.util.List<ExperimentIdentifier>
listExperiments(java.lang.String sessionToken)
Return the list of all visible experiments, along with their hierarchical context (space, project).java.util.List<ExperimentIdentifier>
listExperiments(java.lang.String sessionToken, java.lang.String userId)
Return the list of all experiments visible to user userId, along with their hierarchical context (space, project).java.util.List<FeatureVectorDatasetReference>
listFeatureVectorDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates)
For a given set of plates (given by space / plate bar code), provide the list of all data sets containing feature vectors for each of these plates.java.util.List<ImageDatasetReference>
listImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates)
For a given set of plates provide the list of all data sets containing images for each of these plates.java.util.List<ImageDatasetMetadata>
listImageMetadata(java.lang.String sessionToken, java.util.List<? extends IImageDatasetIdentifier> imageDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listImageMetadata(String, List)
method for each group of objects on appropriate data store server.java.util.List<PlateWellMaterialMapping>
listPlateMaterialMapping(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates, MaterialTypeIdentifier materialTypeIdentifierOrNull)
For a given list of plates, return the mapping of plate wells to materials contained in each well.java.util.List<Plate>
listPlates(java.lang.String sessionToken)
Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).java.util.List<Plate>
listPlates(java.lang.String sessionToken, ExperimentIdentifier experiment)
Return the list of all plates assigned to the given experiment.java.util.List<PlateWellReferenceWithDatasets>
listPlateWells(java.lang.String sessionToken, ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, boolean findDatasets)
For the given experimentIdentifier, find all plate locations that are connected to the specified materialIdentifier.java.util.List<PlateWellReferenceWithDatasets>
listPlateWells(java.lang.String sessionToken, MaterialIdentifier materialIdentifier, boolean findDatasets)
For the given materialIdentifier, find all plate locations that are connected to it.java.util.List<WellIdentifier>
listPlateWells(java.lang.String sessionToken, PlateIdentifier plateIdentifier)
For the given plateIdentifier find all wells that are connected to it.java.util.List<ImageDatasetReference>
listRawImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates)
For a given set of plates provide the list of all data sets containing raw images for each of these plates.java.util.List<ImageDatasetReference>
listSegmentationImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates)
For a given set of plates provide the list of all data sets containing segmentation images for each of these plates.java.util.List<FeatureVectorDataset>
loadFeatures(java.lang.String sessionToken, java.util.List<FeatureVectorDatasetReference> featureDatasets, java.util.List<java.lang.String> featureCodes)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadFeatures(String, List, List)
method for each group of objects on appropriate data store server.java.util.List<FeatureVectorWithDescription>
loadFeaturesForDatasetWellReferences(java.lang.String sessionToken, java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences, java.util.List<java.lang.String> featureCodes)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadFeaturesForDatasetWellReferences(String, List, List)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, boolean convertToPng)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, boolean)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, IImageRepresentationFormatSelectionCriterion... criteria)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, IImageRepresentationFormatSelectionCriterion...)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, ImageRepresentationFormat)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageSize size)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, ImageSize)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, LoadImageConfiguration configuration)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, LoadImageConfiguration)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadPhysicalThumbnailsBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadPhysicalThumbnailsBase64(String, List, ImageRepresentationFormat)
method for each group of objects on appropriate data store server.java.util.List<java.lang.String>
loadThumbnailImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadThumbnailImagesBase64(String, List)
method for each group of objects on appropriate data store server.void
logoutScreening(java.lang.String sessionToken)
Logout the session with the specified session token.java.lang.String
tryLoginScreening(java.lang.String userId, java.lang.String userPassword)
Authenticates the user with a given password.
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Field Detail
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SERVICE_NAME
static final java.lang.String SERVICE_NAME
Name of this service for which it is registered at the RPC name server.- See Also:
- Constant Field Values
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MAJOR_VERSION
static final int MAJOR_VERSION
The major version of this service.- See Also:
- Constant Field Values
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SERVICE_URL
static final java.lang.String SERVICE_URL
Service part of the URL to access this service remotely.- See Also:
- Constant Field Values
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JSON_SERVICE_URL
static final java.lang.String JSON_SERVICE_URL
- See Also:
- Constant Field Values
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Method Detail
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tryLoginScreening
@Transactional java.lang.String tryLoginScreening(java.lang.String userId, java.lang.String userPassword) throws java.lang.IllegalArgumentException
Authenticates the user with a given password.- Returns:
- sessionToken if authentication succeeded,
null
otherwise. - Throws:
java.lang.IllegalArgumentException
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logoutScreening
@Transactional(readOnly=true) void logoutScreening(java.lang.String sessionToken) throws java.lang.IllegalArgumentException
Logout the session with the specified session token.- Throws:
java.lang.IllegalArgumentException
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listPlates
@Transactional(readOnly=true) java.util.List<Plate> listPlates(java.lang.String sessionToken) throws java.lang.IllegalArgumentException
Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).- Throws:
java.lang.IllegalArgumentException
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listPlates
@Transactional(readOnly=true) java.util.List<Plate> listPlates(java.lang.String sessionToken, ExperimentIdentifier experiment) throws java.lang.IllegalArgumentException
Return the list of all plates assigned to the given experiment.- Throws:
java.lang.IllegalArgumentException
- Since:
- 1.5
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getPlateMetadataList
@Transactional(readOnly=true) java.util.List<PlateMetadata> getPlateMetadataList(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates) throws java.lang.IllegalArgumentException
Fetches the contents of a given list of plates. The result will contain well and material properties.- Throws:
java.lang.IllegalArgumentException
- Since:
- 1.8
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listExperiments
@Transactional(readOnly=true) java.util.List<ExperimentIdentifier> listExperiments(java.lang.String sessionToken)
Return the list of all visible experiments, along with their hierarchical context (space, project).- Since:
- 1.1
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listExperiments
@Transactional(readOnly=true) java.util.List<ExperimentIdentifier> listExperiments(java.lang.String sessionToken, java.lang.String userId)
Return the list of all experiments visible to user userId, along with their hierarchical context (space, project).- Since:
- 1.6
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listFeatureVectorDatasets
@Transactional(readOnly=true) java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates) throws java.lang.IllegalArgumentException
For a given set of plates (given by space / plate bar code), provide the list of all data sets containing feature vectors for each of these plates.- Throws:
java.lang.IllegalArgumentException
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listImageDatasets
@Transactional(readOnly=true) java.util.List<ImageDatasetReference> listImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates) throws java.lang.IllegalArgumentException
For a given set of plates provide the list of all data sets containing images for each of these plates.- Throws:
java.lang.IllegalArgumentException
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getImageInfo
@Transactional(readOnly=true) java.util.Map<java.lang.String,LogicalImageInfo> getImageInfo(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCode)
Returns information about logical image in the given image datasets.
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getImageResolutions
@Transactional(readOnly=true) java.util.Map<java.lang.String,java.util.List<ImageResolution>> getImageResolutions(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCode)
Returns information about available image resolutions for the given image datasets.
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listRawImageDatasets
@Transactional(readOnly=true) java.util.List<ImageDatasetReference> listRawImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates) throws java.lang.IllegalArgumentException
For a given set of plates provide the list of all data sets containing raw images for each of these plates.- Throws:
java.lang.IllegalArgumentException
- Since:
- 1.6
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listSegmentationImageDatasets
@Transactional(readOnly=true) java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates) throws java.lang.IllegalArgumentException
For a given set of plates provide the list of all data sets containing segmentation images for each of these plates.- Throws:
java.lang.IllegalArgumentException
- Since:
- 1.6
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getDatasetIdentifiers
@Transactional(readOnly=true) java.util.List<IDatasetIdentifier> getDatasetIdentifiers(java.lang.String sessionToken, java.util.List<java.lang.String> datasetCodes)
Converts a given list of dataset codes to dataset identifiers.
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listPlateWells
@Transactional(readOnly=true) java.util.List<PlateWellReferenceWithDatasets> listPlateWells(java.lang.String sessionToken, ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, boolean findDatasets)
For the given experimentIdentifier, find all plate locations that are connected to the specified materialIdentifier. IffindDatasets == true
, find also the connected image and image analysis data sets for the relevant plates.- Since:
- 1.1
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listPlateWells
@Transactional(readOnly=true) java.util.List<PlateWellReferenceWithDatasets> listPlateWells(java.lang.String sessionToken, MaterialIdentifier materialIdentifier, boolean findDatasets)
For the given materialIdentifier, find all plate locations that are connected to it. IffindDatasets == true
, find also the connected image and image analysis data sets for the relevant plates.- Since:
- 1.2
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listPlateWells
@Transactional(readOnly=true) java.util.List<WellIdentifier> listPlateWells(java.lang.String sessionToken, PlateIdentifier plateIdentifier)
For the given plateIdentifier find all wells that are connected to it.- Since:
- 1.3
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getWellSample
@Transactional(readOnly=true) ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample getWellSample(java.lang.String sessionToken, WellIdentifier wellIdentifier)
For a given wellIdentifier, return the correspondingSample
including properties.- Since:
- 1.3
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getPlateSample
@Transactional(readOnly=true) ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample getPlateSample(java.lang.String sessionToken, PlateIdentifier plateIdentifier)
For a given plateIdentifier, return the correspondingSample
.- Since:
- 1.7
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listPlateMaterialMapping
@Transactional(readOnly=true) java.util.List<PlateWellMaterialMapping> listPlateMaterialMapping(java.lang.String sessionToken, java.util.List<? extends PlateIdentifier> plates, MaterialTypeIdentifier materialTypeIdentifierOrNull)
For a given list of plates, return the mapping of plate wells to materials contained in each well.- Parameters:
plates
- The list of plates to get the mapping formaterialTypeIdentifierOrNull
- If notnull
, consider only materials of the given type for the mapping.- Returns:
- A list of well to material mappings, one element for each plate.
- Since:
- 1.2
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getExperimentImageMetadata
@Transactional(readOnly=true) ExperimentImageMetadata getExperimentImageMetadata(java.lang.String sessionToken, ExperimentIdentifier experimentIdentifer)
Returns aggregated metadata for all images/plates within one experiment.- Since:
- 1.9
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listAvailableFeatureCodes
@Transactional(readOnly=true) java.util.List<java.lang.String> listAvailableFeatureCodes(java.lang.String sessionToken, java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableFeatureCodes(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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listAvailableFeatures
@Transactional(readOnly=true) java.util.List<FeatureInformation> listAvailableFeatures(java.lang.String sessionToken, java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableFeatures(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadFeatures
@Transactional(readOnly=true) java.util.List<FeatureVectorDataset> loadFeatures(java.lang.String sessionToken, java.util.List<FeatureVectorDatasetReference> featureDatasets, java.util.List<java.lang.String> featureCodes)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadFeatures(String, List, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadFeaturesForDatasetWellReferences
@Transactional(readOnly=true) java.util.List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(java.lang.String sessionToken, java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences, java.util.List<java.lang.String> featureCodes)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadFeaturesForDatasetWellReferences(String, List, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, boolean convertToPng)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, boolean)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadThumbnailImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadThumbnailImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadThumbnailImagesBase64(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageSize size)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, ImageSize)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, LoadImageConfiguration configuration)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, LoadImageConfiguration)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, ImageRepresentationFormat)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadImagesBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadImagesBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, IImageRepresentationFormatSelectionCriterion... criteria)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadImagesBase64(String, List, IImageRepresentationFormatSelectionCriterion...)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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listImageMetadata
@Transactional(readOnly=true) java.util.List<ImageDatasetMetadata> listImageMetadata(java.lang.String sessionToken, java.util.List<? extends IImageDatasetIdentifier> imageDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listImageMetadata(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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listAvailableImageRepresentationFormats
@Transactional(readOnly=true) java.util.List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(java.lang.String sessionToken, java.util.List<? extends IDatasetIdentifier> imageDatasets)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.listAvailableImageRepresentationFormats(String, List)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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loadPhysicalThumbnailsBase64
@Transactional(readOnly=true) java.util.List<java.lang.String> loadPhysicalThumbnailsBase64(java.lang.String sessionToken, java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format)
Groups the specified objects by a data store code and callsIDssServiceRpcScreening.loadPhysicalThumbnailsBase64(String, List, ImageRepresentationFormat)
method for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.- Since:
- 1.10
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