ScreeningOpenbisServiceFacade

java.lang.Object
- ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade

All Implemented Interfaces:

IScreeningOpenbisServiceFacade
```
public class ScreeningOpenbisServiceFacade
extends java.lang.Object
implements IScreeningOpenbisServiceFacade
```
A client side facade of openBIS and Datastore Server API.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static interface`	`ScreeningOpenbisServiceFacade.IImageOutputStreamProvider` An interface to provide mapping between image references and output streams where the images should be saved.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`clearWellImageCache()` Removes all images loaded by `IScreeningOpenbisServiceFacade.loadImageWellCaching(PlateImageReference, ImageSize)` and `IScreeningOpenbisServiceFacade.loadThumbnailImageWellCaching(PlateImageReference)` from the image cache, thus freeing the memory.
`java.util.List<FeatureVectorDatasetWellReference>`	`convertToFeatureVectorDatasetWellIdentifier(java.util.List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets)` Converts the given list of `PlateWellReferenceWithDatasets` into a list of `FeatureVectorDatasetWellReference`.
`java.util.List<WellPosition>`	`convertToWellPositions(java.util.List<WellIdentifier> wellIds)` Converts the given `WellIdentifiers` to `WellPositions`
`java.util.List<PlateImageReference>`	`createPlateImageReferences(IImageDatasetIdentifier imageDatasetId, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsToUse)` Returns the list of all plate image references for the given `imageDatasetId` (all tiles), and the given `channelCodesOrNull` and `wellsToUse`.
`java.util.List<PlateImageReference>`	`createPlateImageReferences(IImageDatasetIdentifier imageDatasetId, java.util.List<java.lang.String> channeldCodesOrNull, java.util.List<WellPosition> wellsToUse)` Returns the list of all plate image references for the given `imageDatasetId` (all tiles), and the given `channelCodesOrNull` and `wellsToUse`.
`java.util.List<PlateImageReference>`	`createPlateImageReferences(ImageDatasetReference imageDatasetRef)` Returns the list of all plate image references for the given `imageDatasetRef`.
`java.util.List<PlateImageReference>`	`createPlateImageReferences(ImageDatasetReference imageDatasetRef, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)` Returns the list of all plate image references for the given `imageDatasetRef` (all tiles), the given `channelCodesOrNull` and `wellsOrNull`.
`java.util.List<PlateImageReference>`	`createPlateImageReferences(ImageDatasetReference imageDatasetRef, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)` Returns the list of all plate image references for the given `imageDatasetRef` (all tiles), the given `channelCodesOrNull` and `wellsOrNull`.
`ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss`	`getDataSet(java.lang.String dataSetCode)`
`java.util.List<IDatasetIdentifier>`	`getDatasetIdentifiers(java.util.List<java.lang.String> datasetCodes)` Converts a given list of dataset codes to dataset identifiers which can be used in other API calls.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet>`	`getDataSetMetaData(java.util.List<java.lang.String> dataSetCodes)` Returns meta data for all specified data set codes.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss>`	`getDataSets(ExperimentIdentifier experimentIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter filter)` Gets proxies to the data sets owned by specified experiment and passing specified filter.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss>`	`getDataSets(PlateIdentifier plateIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)` Gets proxies to the data sets owned by specified plate and passing specified filter.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss>`	`getDataSets(PlateIdentifier plateIdentifier, java.lang.String datasetTypeCodePattern)` Get proxies to the data sets owned by specified plate.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss>`	`getDataSets(WellIdentifier wellIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)` Gets proxies to the data sets owned by specified well and passing specified filter..
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss>`	`getDataSets(WellIdentifier wellIdentifier, java.lang.String datasetTypeCodePattern)` Get proxies to the data sets owned by specified well.
`ExperimentImageMetadata`	`getExperimentImageMetadata(ExperimentIdentifier experimentIdentifier)` Returns aggregated metadata for all images/plates within one experiment.
`java.util.List<java.lang.String>`	`getFeatureList(IFeatureVectorDatasetIdentifier featureDataset, java.lang.String featureListCode)` Return the feature codes from the specified feature list of a specified feature data set
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet>`	`getFullDataSets(ExperimentIdentifier experimentIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)` A list of data sets owned by specified experiment and passing specified filter.
`java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet>`	`getFullDataSets(PlateIdentifier plateIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)` A list of data sets owned by specified plate and passing specified filter.
`ch.systemsx.cisd.base.image.IImageTransformerFactory`	`getImageTransformerFactoryOrNull(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel)` Returns the transformer factory for the specified channel and the experiment to which the specified data sets belong.
`java.util.List<PlateMetadata>`	`getPlateMetadataList(java.util.List<? extends PlateIdentifier> plateIdentifiers)` Return full metadata for each specified plate, including wells and their properties.
`java.lang.String`	`getSessionToken()` Return the session token for this authenticated user.
`java.util.Map<java.lang.String,java.lang.String>`	`getWellProperties(WellIdentifier wellIdentifier)` Returns all properties of specified well as a map.
`java.util.List<java.lang.String>`	`listAnalysisProcedures(ExperimentIdentifier experimentIdentifier)` Returns an alphabetically sorted list of analysis procedure codes of all data sets of the specified experiment.
`java.util.List<java.lang.String>`	`listAvailableFeatureCodes(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)` For a given set of feature vector data sets provides the list of all available features.
`java.util.List<java.lang.String>`	`listAvailableFeatureNames(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)` For a given set of feature vector data sets provides the list of all available features.
`java.util.List<FeatureInformation>`	`listAvailableFeatures(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)` For a given set of feature vector data sets provide the list of all available features.
`java.util.List<DatasetImageRepresentationFormats>`	`listAvailableImageRepresentationFormats(java.util.List<? extends IDatasetIdentifier> dataSetIdentifiers)`
`java.util.List<ExperimentIdentifier>`	`listExperiments()` Return the list of all visible experiments, along with their hierarchical context (space, project).
`java.util.List<ExperimentIdentifier>`	`listExperiments(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.util.List<? extends PlateIdentifier> plates)` For a given set of plates provides the list of all connected data sets containing feature vectors.
`java.util.List<FeatureVectorDatasetReference>`	`listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)` For a given set of plates provides the list of all connected data sets containing feature vectors and having specified analysis procedure property.
`java.util.List<ImageDatasetReference>`	`listImageDatasets(java.util.List<? extends PlateIdentifier> plates)` Deprecated. Use `listRawImageDatasets(List)` instead.
`ImageDatasetMetadata`	`listImageMetadata(IImageDatasetIdentifier imageDataset)` For a given image data set, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
`java.util.List<ImageDatasetMetadata>`	`listImageMetadata(java.util.List<? extends IImageDatasetIdentifier> imageDatasets)` For a given set of image data sets, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
`java.util.List<PlateWellMaterialMapping>`	`listPlateMaterialMapping(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()` Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
`java.util.List<Plate>`	`listPlates(ExperimentIdentifier experiment)` Return the list of all plates for the given `experiment`.
`java.util.List<Plate>`	`listPlates(ExperimentIdentifier experiment, java.lang.String analysisProcedure)` Return the list of all plates for the given `experiment` and analysis procedure.
`java.util.List<PlateWellReferenceWithDatasets>`	`listPlateWells(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(MaterialIdentifier materialIdentifier, boolean findDatasets)` For the given `materialIdentifier` find all plate locations that are connected to it.
`java.util.List<WellIdentifier>`	`listPlateWells(PlateIdentifier plateIdentifier)` For the given `plateIdentifier` find all wells that are connected to it.
`java.util.List<ImageDatasetReference>`	`listRawImageDatasets(java.util.List<? extends PlateIdentifier> plates)` For a given set of plates provides the list of all connected data sets containing raw images.
`java.util.List<ImageDatasetReference>`	`listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates)` For a given set of plates provides the list of all connected data sets containing images.
`java.util.List<ImageDatasetReference>`	`listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)` For a given set of plates provides the list of all connected data sets containing segmentation images (overlays) and calculated by specified analysis procedure.
`java.util.List<FeatureVectorDataset>`	`loadFeatures(java.util.List<FeatureVectorDatasetReference> featureDatasets, java.util.List<java.lang.String> featureCodesOrNull)` For a given set of data sets and a set of features (given by their code), provide all the feature vectors.
`java.util.List<FeatureVectorWithDescription>`	`loadFeaturesForDatasetWellReferences(java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences, java.util.List<java.lang.String> featureCodesOrNull)` Conceptually, for a given list of dataset well references (i.e.
`java.util.List<FeatureVectorDataset>`	`loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull)` For a given set of plates and a set of features (given by their code), provide all the feature vectors.
`java.util.List<FeatureVectorDataset>`	`loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull, java.lang.String analysisProcedureOrNull)` For a given set of plates and a set of features (given by their code), provide all the feature vectors created by specified analysis procedure.
`java.util.List<FeatureVectorWithDescription>`	`loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)` For the given `experimentIdentifier` find all plate locations that are connected to the specified `materialIdentifier` and load the feature vectors for the given feature code if not `null`, or all available features otherwise.
`java.util.List<FeatureVectorWithDescription>`	`loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)` For the given `experimentIdentifier` find all plate locations that are connected to the specified `materialIdentifier` and load the feature vectors for the given feature code if not `null`, or all available features otherwise.
`java.util.List<FeatureVectorWithDescription>`	`loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)` For the given `materialIdentifier` find all plate locations that are connected to it and load the feature vectors for the given feature code if not `null`, or all available features otherwise.
`java.util.List<FeatureVectorWithDescription>`	`loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)` For the given `materialIdentifier` find all plate locations that are connected to it and load the feature vectors for the given feature code if not `null`, or all available features otherwise.
`java.util.List<byte[]>`	`loadImages(IDatasetIdentifier dataSetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull)` Loads original images or thumbnails for a specified data set, a list of well positions (empty list means all wells), a channel, and an optional thumb nail size.
`void`	`loadImages(IDatasetIdentifier dataSetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull, IPlateImageHandler plateImageHandler)` Loads PNG-encoded images for specified data set, list of well positions (empty list means all wells), channel, and optional thumb nail size.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, boolean convertToPNG, IPlateImageHandler plateImageHandler)` Loads images for a given list of image references (given by data set code, well position, channel and tile) and hands it over to the `plateImageHandler`. If `convertToPng==true`, the images will be converted to PNG format before being shipped, otherwise they will be shipped in the format that they are stored on the server.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, ImageSize sizeOrNull, IPlateImageHandler plateImageHandler)` Loads PNG-encoded images for specified image references and, optionally, image size.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, IImageRepresentationFormatSelectionCriterion... criteria)` Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and image selection criteria.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, ImageRepresentationFormat format)` Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and specified image representation format.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, LoadImageConfiguration configuration, IPlateImageHandler plateImageHandler)` Loads images where the desired properties of the images are specified by a LoadImageConfiguration.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)` Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
`void`	`loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider, boolean convertToPNG)` Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
`byte[]`	`loadImageWellCaching(PlateImageReference imageReference, ImageSize imageSizeOrNull)` Loads an PNG-encoded image for the specified image reference and, optionally, image size.
`void`	`loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, IPlateImageHandler plateImageHandler)` Retrieves images for the specified image references and invokes the plateImageHandler passing in image data.
`void`	`loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)` Retrieves images for the specified image references and invokes the IImageOutputStreamProvider passing in image data.
`void`	`loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler)` Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
`void`	`loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)` Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams.
`byte[]`	`loadThumbnailImageWellCaching(PlateImageReference imageReference)` Loads the PNG-encoded image for the specified `imageReference`.
`void`	`logout()` Closes connection with the server.
`ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss`	`putDataSet(ExperimentIdentifier experimentIdentifier, java.io.File dataSetFile, ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)` Upload a new data set to the DSS for a plate.
`ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss`	`putDataSet(PlateIdentifier plateIdentifier, java.io.File dataSetFile, ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)` Upload a new data set to the DSS for a plate.
`ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss`	`putDataSet(WellIdentifier wellIdentifier, java.io.File dataSetFile, ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)` Upload a new data set to the DSS for a well.
`void`	`saveImageTransformerFactory(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel, ch.systemsx.cisd.base.image.IImageTransformerFactory transformerFactoryOrNull)` Saves the specified transformer factory for the specified channel and the experiment to which the specified data sets belong.
`static IScreeningOpenbisServiceFacade`	`tryCreate(java.lang.String sessionToken, java.lang.String serverUrl)` Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
`static IScreeningOpenbisServiceFacade`	`tryCreate(java.lang.String userId, java.lang.String userPassword, java.lang.String serverUrl)` Creates a service facade which communicates with the openBIS server at the specified URL.
`static IScreeningOpenbisServiceFacade`	`tryCreateForTest(java.lang.String sessionToken, java.lang.String serverUrl, ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer openbisServer)` This constructor is only for use in tests.
`void`	`updateWellProperties(WellIdentifier wellIdentifier, java.util.Map<java.lang.String,java.lang.String> properties)` Updates properties of specified well.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Method Detail
  - tryCreate
```
public static IScreeningOpenbisServiceFacade tryCreate(java.lang.String userId,
                                       java.lang.String userPassword,
                                       java.lang.String serverUrl)
```
    Creates a service facade which communicates with the openBIS server at the specified URL. Authenticates the user.
    
    Returns:
    null if the user could not be authenticated.
  - tryCreate
```
public static IScreeningOpenbisServiceFacade tryCreate(java.lang.String sessionToken,
                                       java.lang.String serverUrl)
```
    Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
    
    Parameters:
    sessionToken - The session token for the authenticated user
    serverUrl - The URL for the openBIS application server
  - tryCreateForTest
```
public static IScreeningOpenbisServiceFacade tryCreateForTest(java.lang.String sessionToken,
                                              java.lang.String serverUrl,
                                              ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer openbisServer)
```
    This constructor is only for use in tests. Do not use it otherwise.
  - getSessionToken
```
public java.lang.String getSessionToken()
```
    Return the session token for this authenticated user.
    
    Specified by:
    
    getSessionToken in interface IScreeningOpenbisServiceFacade
  - logout
```
public void logout()
```
    Closes connection with the server. After calling this method this facade cannot be used.
    
    Specified by:
    
    logout in interface IScreeningOpenbisServiceFacade
  - clearWellImageCache
```
public void clearWellImageCache()
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Removes all images loaded by IScreeningOpenbisServiceFacade.loadImageWellCaching(PlateImageReference, ImageSize) and IScreeningOpenbisServiceFacade.loadThumbnailImageWellCaching(PlateImageReference) from the image cache, thus freeing the memory.
    
    Specified by:
    
    clearWellImageCache in interface IScreeningOpenbisServiceFacade
  - listPlates
```
public java.util.List<Plate> listPlates()
```
    Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
    
    Specified by:
    
    listPlates in interface IScreeningOpenbisServiceFacade
  - getPlateMetadataList
```
public java.util.List<PlateMetadata> getPlateMetadataList(java.util.List<? extends PlateIdentifier> plateIdentifiers)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Return full metadata for each specified plate, including wells and their properties. If a well contains a material, its properties are also available.
    
    Specified by:
    
    getPlateMetadataList in interface IScreeningOpenbisServiceFacade
  - listPlates
```
public java.util.List<Plate> listPlates(ExperimentIdentifier experiment)
```
    Return the list of all plates for the given experiment.
    
    Specified by:
    
    listPlates in interface IScreeningOpenbisServiceFacade
  - listPlates
```
public java.util.List<Plate> listPlates(ExperimentIdentifier experiment,
                               java.lang.String analysisProcedure)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Return the list of all plates for the given experiment and analysis procedure. Each returned plate has at least one data set with the specified analysis procedure.
    
    Specified by:
    
    listPlates in interface IScreeningOpenbisServiceFacade
  - listExperiments
```
public java.util.List<ExperimentIdentifier> listExperiments()
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Return the list of all visible experiments, along with their hierarchical context (space, project).
    
    Specified by:
    
    listExperiments in interface IScreeningOpenbisServiceFacade
  - listExperiments
```
public java.util.List<ExperimentIdentifier> listExperiments(java.lang.String userId)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Return the list of all experiments visible to user userId, along with their hierarchical context (space, project).
    The user calling this method needs to have a role INSTANCE_OBSERVER on the openBIS instance.
    
    Specified by:
    
    listExperiments in interface IScreeningOpenbisServiceFacade
  - listFeatureVectorDatasets
```
public java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates)
```
    For a given set of plates provides the list of all connected data sets containing feature vectors.
    
    Specified by:
    
    listFeatureVectorDatasets in interface IScreeningOpenbisServiceFacade
  - listFeatureVectorDatasets
```
public java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates,
                                                                      java.lang.String analysisProcedureOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given set of plates provides the list of all connected data sets containing feature vectors and having specified analysis procedure property.
    
    Specified by:
    
    listFeatureVectorDatasets in interface IScreeningOpenbisServiceFacade
    
    analysisProcedureOrNull - If null returned list isn't filtered on analysis procedure property.
  - listImageDatasets
```
@Deprecated
public java.util.List<ImageDatasetReference> listImageDatasets(java.util.List<? extends PlateIdentifier> plates)
```
    Deprecated. Use listRawImageDatasets(List) instead.
    
    For a given set of plates provides the list of all connected data sets containing raw images.
    
    Specified by:
    
    listImageDatasets in interface IScreeningOpenbisServiceFacade
  - listRawImageDatasets
```
public java.util.List<ImageDatasetReference> listRawImageDatasets(java.util.List<? extends PlateIdentifier> plates)
```
    For a given set of plates provides the list of all connected data sets containing raw images.
    
    Specified by:
    
    listRawImageDatasets in interface IScreeningOpenbisServiceFacade
  - listSegmentationImageDatasets
```
public java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates)
```
    For a given set of plates provides the list of all connected data sets containing images.
    
    Specified by:
    
    listSegmentationImageDatasets in interface IScreeningOpenbisServiceFacade
  - listSegmentationImageDatasets
```
public java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates,
                                                                  java.lang.String analysisProcedureOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given set of plates provides the list of all connected data sets containing segmentation images (overlays) and calculated by specified analysis procedure.
    
    Specified by:
    
    listSegmentationImageDatasets in interface IScreeningOpenbisServiceFacade
    
    analysisProcedureOrNull - If null no restriction applies.
  - listPlateWells
```
public java.util.List<PlateWellReferenceWithDatasets> listPlateWells(ExperimentIdentifier experimentIdentifer,
                                                            MaterialIdentifier materialIdentifier,
                                                            boolean findDatasets)
```
    For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier. If findDatasets == true, find also the connected image and image analysis data sets for the relevant plates.
    
    Specified by:
    
    listPlateWells in interface IScreeningOpenbisServiceFacade
  - listPlateWells
```
public java.util.List<PlateWellReferenceWithDatasets> listPlateWells(MaterialIdentifier materialIdentifier,
                                                            boolean findDatasets)
```
    For the given materialIdentifier find all plate locations that are connected to it. If findDatasets == true, find also the connected image and image analysis data sets for the relevant plates.
    
    Specified by:
    
    listPlateWells in interface IScreeningOpenbisServiceFacade
  - listPlateWells
```
public java.util.List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier)
```
    For the given plateIdentifier find all wells that are connected to it.
    
    Specified by:
    
    listPlateWells in interface IScreeningOpenbisServiceFacade
  - getWellProperties
```
public java.util.Map<java.lang.String,java.lang.String> getWellProperties(WellIdentifier wellIdentifier)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns all properties of specified well as a map.
    
    Specified by:
    
    getWellProperties in interface IScreeningOpenbisServiceFacade
  - updateWellProperties
```
public void updateWellProperties(WellIdentifier wellIdentifier,
                        java.util.Map<java.lang.String,java.lang.String> properties)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Updates properties of specified well.
    
    Specified by:
    
    updateWellProperties in interface IScreeningOpenbisServiceFacade
  - getDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
                                                                                 java.lang.String datasetTypeCodePattern)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Get proxies to the data sets owned by specified well.
    
    Specified by:
    
    getDataSets in interface IScreeningOpenbisServiceFacade
    
    datasetTypeCodePattern - only datasets of the type which matche the specified pattern will be returned. To fetch all datasets specify ".*".
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(WellIdentifier wellIdentifier,
                                                                                 ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Gets proxies to the data sets owned by specified well and passing specified filter..
    
    Specified by:
    
    getDataSets in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getDataSet
```
public ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss getDataSet(java.lang.String dataSetCode)
                                                                  throws java.lang.IllegalStateException,
                                                                         ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Specified by:
    
    getDataSet in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.lang.IllegalStateException
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
  - getDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
                                                                                 java.lang.String datasetTypeCodePattern)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Get proxies to the data sets owned by specified plate.
    
    Specified by:
    
    getDataSets in interface IScreeningOpenbisServiceFacade
    
    datasetTypeCodePattern - only datasets of the type which matche the specified pattern will be returned. To fetch all datasets specify ".*".
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(PlateIdentifier plateIdentifier,
                                                                                 ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Gets proxies to the data sets owned by specified plate and passing specified filter.
    
    Specified by:
    
    getDataSets in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getFullDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getFullDataSets(PlateIdentifier plateIdentifier,
                                                                                 ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    A list of data sets owned by specified plate and passing specified filter. The data set objects provide metadata (e.g. code, properties etc. from the openBIS AS) as well as data (e.g. files from openBIS DSS).
    
    Specified by:
    
    getFullDataSets in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(ExperimentIdentifier experimentIdentifier,
                                                                                 ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter filter)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Gets proxies to the data sets owned by specified experiment and passing specified filter.
    
    Specified by:
    
    getDataSets in interface IScreeningOpenbisServiceFacade
  - getFullDataSets
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getFullDataSets(ExperimentIdentifier experimentIdentifier,
                                                                                 ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)
                                                                                   throws java.lang.IllegalStateException,
                                                                                          ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    A list of data sets owned by specified experiment and passing specified filter. The data set objects provide metadata (e.g. code, properties etc. from the openBIS AS) as well as data (e.g. files from openBIS DSS).
    
    Specified by:
    
    getFullDataSets in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
  - getDataSetMetaData
```
public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getDataSetMetaData(java.util.List<java.lang.String> dataSetCodes)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns meta data for all specified data set codes. This contains data set type, properties, and codes of linked parent and children data sets.
    
    Specified by:
    
    getDataSetMetaData in interface IScreeningOpenbisServiceFacade
    
    Returns:
    result in the same order as the list of data set codes.
  - putDataSet
```
public ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss putDataSet(WellIdentifier wellIdentifier,
                                                                java.io.File dataSetFile,
                                                                ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)
                                                                  throws java.lang.IllegalStateException,
                                                                         ch.systemsx.cisd.common.exceptions.EnvironmentFailureException,
                                                                         java.io.IOException
```
    Upload a new data set to the DSS for a well.
    
    Specified by:
    
    putDataSet in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    wellIdentifier - Identifier of a well that should become owner of the new data set
    dataSetFile - A file or folder containing the data
    dataSetMetadataOrNull - The optional metadata overriding server defaults for the new data set
    
    Returns:
    A proxy to the newly added data set
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
    
    java.io.IOException - when accessing the data set file or folder fails
  - putDataSet
```
public ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss putDataSet(PlateIdentifier plateIdentifier,
                                                                java.io.File dataSetFile,
                                                                ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)
                                                                  throws java.lang.IllegalStateException,
                                                                         ch.systemsx.cisd.common.exceptions.EnvironmentFailureException,
                                                                         java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Upload a new data set to the DSS for a plate.
    
    Specified by:
    
    putDataSet in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    plateIdentifier - Identifier of a plate that should become owner of the new data set
    dataSetFile - A file or folder containing the data
    dataSetMetadataOrNull - The optional metadata overriding server defaults for the new data set
    
    Returns:
    A proxy to the newly added data set
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
    
    java.io.IOException - when accessing the data set file or folder fails
  - putDataSet
```
public ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss putDataSet(ExperimentIdentifier experimentIdentifier,
                                                                java.io.File dataSetFile,
                                                                ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetMetadataDTO dataSetMetadataOrNull)
                                                                  throws java.lang.IllegalStateException,
                                                                         ch.systemsx.cisd.common.exceptions.EnvironmentFailureException,
                                                                         java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Upload a new data set to the DSS for a plate.
    
    Specified by:
    
    putDataSet in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    experimentIdentifier - Identifier of a experiment that should become owner of the new data set
    dataSetFile - A file or folder containing the data
    dataSetMetadataOrNull - The optional metadata overriding server defaults for the new data set
    
    Returns:
    A proxy to the newly added data set
    
    Throws:
    
    java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.
    
    ch.systemsx.cisd.common.exceptions.EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.
    
    java.io.IOException - when accessing the data set file or folder fails
  - getDatasetIdentifiers
```
public java.util.List<IDatasetIdentifier> getDatasetIdentifiers(java.util.List<java.lang.String> datasetCodes)
```
    Converts a given list of dataset codes to dataset identifiers which can be used in other API calls.
    
    Specified by:
    
    getDatasetIdentifiers in interface IScreeningOpenbisServiceFacade
  - listAvailableFeatureNames
```
public java.util.List<java.lang.String> listAvailableFeatureNames(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given set of feature vector data sets provides the list of all available features. This is just the name of the feature. If for different data sets different sets of features are available, provides the union of the feature names of all data sets.
    
    Specified by:
    
    listAvailableFeatureNames in interface IScreeningOpenbisServiceFacade
  - listAvailableFeatureCodes
```
public java.util.List<java.lang.String> listAvailableFeatureCodes(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
```
    For a given set of feature vector data sets provides the list of all available features. This is just the code of the feature. If for different data sets different sets of features are available, provides the union of the feature names of all data sets.
    
    Specified by:
    
    listAvailableFeatureCodes in interface IScreeningOpenbisServiceFacade
  - getFeatureList
```
public java.util.List<java.lang.String> getFeatureList(IFeatureVectorDatasetIdentifier featureDataset,
                                              java.lang.String featureListCode)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Return the feature codes from the specified feature list of a specified feature data set
    
    Specified by:
    
    getFeatureList in interface IScreeningOpenbisServiceFacade
  - listAvailableFeatures
```
public java.util.List<FeatureInformation> listAvailableFeatures(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
```
    For a given set of feature vector data sets provide the list of all available features. This contains the code, label and description of the feature. If for different data sets different sets of features are available, provide the union of the features of all data sets. Only available when all data store services have minor version 9 or newer.
    
    Specified by:
    
    listAvailableFeatures in interface IScreeningOpenbisServiceFacade
  - loadFeaturesForPlates
```
public java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates,
                                                         java.util.List<java.lang.String> featureCodesOrNull)
```
    For a given set of plates and a set of features (given by their code), provide all the feature vectors.
    
    Specified by:
    
    loadFeaturesForPlates in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    plates - The plates to get the feature vectors for
    featureCodesOrNull - The codes of the features to load, or null, if all available features should be loaded.
    
    Returns:
    The list of FeatureVectorDatasets, each element corresponds to one of the featureDatasets.
  - loadFeaturesForPlates
```
public java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates,
                                                         java.util.List<java.lang.String> featureCodesOrNull,
                                                         java.lang.String analysisProcedureOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given set of plates and a set of features (given by their code), provide all the feature vectors created by specified analysis procedure.
    
    Specified by:
    
    loadFeaturesForPlates in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    plates - The plates to get the feature vectors for
    featureCodesOrNull - The codes of the features to load, or null, if all available features should be loaded.
    analysisProcedureOrNull - If null result isn't restricted to any analysis procedure.
    
    Returns:
    The list of FeatureVectorDatasets, each element corresponds to one of the featureDatasets.
  - loadFeatures
```
public java.util.List<FeatureVectorDataset> loadFeatures(java.util.List<FeatureVectorDatasetReference> featureDatasets,
                                                java.util.List<java.lang.String> featureCodesOrNull)
```
    For a given set of data sets and a set of features (given by their code), provide all the feature vectors.
    
    Specified by:
    
    loadFeatures in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    featureDatasets - The data sets to get the feature vectors for
    featureCodesOrNull - The codes of the features to load, or null, if all available features should be loaded.
    
    Returns:
    The list of FeatureVectorDatasets, each element corresponds to one of the featureDatasets.
  - convertToFeatureVectorDatasetWellIdentifier
```
public java.util.List<FeatureVectorDatasetWellReference> convertToFeatureVectorDatasetWellIdentifier(java.util.List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Converts the given list of PlateWellReferenceWithDatasets into a list of FeatureVectorDatasetWellReference.
    
    Specified by:
    
    convertToFeatureVectorDatasetWellIdentifier in interface IScreeningOpenbisServiceFacade
    
    See Also:
    IScreeningOpenbisServiceFacade.listPlateWells(ExperimentIdentifier, MaterialIdentifier, boolean), IScreeningOpenbisServiceFacade.loadFeaturesForDatasetWellReferences(List, List)
  - loadFeaturesForDatasetWellReferences
```
public java.util.List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences,
                                                                                java.util.List<java.lang.String> featureCodesOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Conceptually, for a given list of dataset well references (i.e. specified wells on specified feature vector data sets) and a set of features (given by their code) provide the feature matrix. In this matrix, each column is one feature, each row is one well in one data set.
    Physically, the result is delivered as a list of feature vectors. Each entry in this list corresponds to one well in one dataset.
    
    Specified by:
    
    loadFeaturesForDatasetWellReferences in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    datasetWellReferences - The references for datasets / wells to get the feature vectors for.
    featureCodesOrNull - The codes of the features to build the feature vectors from, or null, if all available features should be included. Note that for an empty list as well all features will be included.
    
    Returns:
    The list of FeatureVectorWithDescriptions, each element corresponds to one of the datasetWellReferences. Note that the order of the returned list is not guaranteed to be the same as the order of the list datasetWellReferences. Use FeatureVectorWithDescription.getDatasetWellReference() to find the corresponding dataset / well.
  - loadFeaturesForPlateWells
```
public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer,
                                                                     MaterialIdentifier materialIdentifier,
                                                                     java.util.List<java.lang.String> featureCodesOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier and load the feature vectors for the given feature code if not null, or all available features otherwise.
    
    Specified by:
    
    loadFeaturesForPlateWells in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    experimentIdentifer - The identifier of the experiment to get the feature vectors for
    materialIdentifier - The identifier of the material contained in the wells to get the feature vectors for.
    featureCodesOrNull - The codes of the features to build the feature vectors from, or null, if all available features should be included. Note that for an empty list as well all features will be included.
    
    Returns:
    The list of FeatureVectorWithDescriptions found in the given experimentIdentifer and connected with the given materialIdentifier.
  - loadFeaturesForPlateWells
```
public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer,
                                                                     MaterialIdentifier materialIdentifier,
                                                                     java.lang.String analysisProcedureOrNull,
                                                                     java.util.List<java.lang.String> featureCodesOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For the given experimentIdentifier find all plate locations that are connected to the specified materialIdentifier and load the feature vectors for the given feature code if not null, or all available features otherwise. Do this only for data sets with specified value of property ANALYSIS_PROCEDURE, if not null.
    
    Specified by:
    
    loadFeaturesForPlateWells in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    experimentIdentifer - The identifier of the experiment to get the feature vectors for
    materialIdentifier - The identifier of the material contained in the wells to get the feature vectors for.
    analysisProcedureOrNull - If not null result is restricted to data sets with property ANALYSIS_PROCEDURE set to this value.
    featureCodesOrNull - The codes of the features to build the feature vectors from, or null, if all available features should be included. Note that for an empty list as well all features will be included.
    
    Returns:
    The list of FeatureVectorWithDescriptions found in the given experimentIdentifer and connected with the given materialIdentifier.
  - loadFeaturesForPlateWells
```
public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier,
                                                                     java.util.List<java.lang.String> featureCodesOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For the given materialIdentifier find all plate locations that are connected to it and load the feature vectors for the given feature code if not null, or all available features otherwise.
    
    Specified by:
    
    loadFeaturesForPlateWells in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    materialIdentifier - The identifier of the material contained in the wells to get the feature vectors for.
    featureCodesOrNull - The codes of the features to build the feature vectors from, or null, if all available features should be included. Note that for an empty list as well all features will be included.
    
    Returns:
    The list of FeatureVectorWithDescriptions found in the given experimentIdentifer and connected with the given materialIdentifier.
  - loadFeaturesForPlateWells
```
public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier,
                                                                     java.lang.String analysisProcedureOrNull,
                                                                     java.util.List<java.lang.String> featureCodesOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For the given materialIdentifier find all plate locations that are connected to it and load the feature vectors for the given feature code if not null, or all available features otherwise. Do this only for data sets with specified value of property ANALYSIS_PROCEDURE, if not null.
    
    Specified by:
    
    loadFeaturesForPlateWells in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    materialIdentifier - The identifier of the material contained in the wells to get the feature vectors for.
    analysisProcedureOrNull - If not null result is restricted to data sets with property ANALYSIS_PROCEDURE set to this value.
    featureCodesOrNull - The codes of the features to build the feature vectors from, or null, if all available features should be included. Note that for an empty list as well all features will be included.
    
    Returns:
    The list of FeatureVectorWithDescriptions found in the given experimentIdentifer and connected with the given materialIdentifier.
  - convertToWellPositions
```
public java.util.List<WellPosition> convertToWellPositions(java.util.List<WellIdentifier> wellIds)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Converts the given WellIdentifiers to WellPositions
    
    Specified by:
    
    convertToWellPositions in interface IScreeningOpenbisServiceFacade
  - createPlateImageReferences
```
public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the list of all plate image references for the given imageDatasetRef.
    
    Specified by:
    
    createPlateImageReferences in interface IScreeningOpenbisServiceFacade
  - createPlateImageReferences
```
public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef,
                                                             java.util.List<java.lang.String> channelCodesOrNull,
                                                             java.util.List<WellPosition> wellsOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the list of all plate image references for the given imageDatasetRef (all tiles), the given channelCodesOrNull and wellsOrNull.
    
    Specified by:
    
    createPlateImageReferences in interface IScreeningOpenbisServiceFacade
    
    channelCodesOrNull - The channel codes for which to create image references. If null or empty, references for all channels will be created.
    wellsOrNull - The wells to create image references for. If null or empty, references for all wells will be created.
  - createPlateImageReferences
```
public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef,
                                                             ImageDatasetMetadata metadataOrNull,
                                                             java.util.List<java.lang.String> channelCodesOrNull,
                                                             java.util.List<WellPosition> wellsOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the list of all plate image references for the given imageDatasetRef (all tiles), the given channelCodesOrNull and wellsOrNull.
    
    Specified by:
    
    createPlateImageReferences in interface IScreeningOpenbisServiceFacade
    
    metadataOrNull - The metadata of the image dataset. If null, the metadata will be fetched from the server.
    channelCodesOrNull - The channel codes for which to create image references. If null or empty, references for all channels will be created.
    wellsOrNull - The wells to create image references for. If null or empty, references for all wells will be created.
  - createPlateImageReferences
```
public java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetId,
                                                             java.util.List<java.lang.String> channeldCodesOrNull,
                                                             java.util.List<WellPosition> wellsToUse)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the list of all plate image references for the given imageDatasetId (all tiles), and the given channelCodesOrNull and wellsToUse.
    
    Specified by:
    
    createPlateImageReferences in interface IScreeningOpenbisServiceFacade
    
    channeldCodesOrNull - The channel codes for which to create image references. If null or empty, references for all channels will be created.
    wellsToUse - The wells to create image references for. Must not be null.
  - createPlateImageReferences
```
public java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetId,
                                                             ImageDatasetMetadata metadataOrNull,
                                                             java.util.List<java.lang.String> channelCodesOrNull,
                                                             java.util.List<WellPosition> wellsToUse)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the list of all plate image references for the given imageDatasetId (all tiles), and the given channelCodesOrNull and wellsToUse.
    
    Specified by:
    
    createPlateImageReferences in interface IScreeningOpenbisServiceFacade
    
    metadataOrNull - The metadata of the image dataset. If null, the metadata will be fetched from the server.
    channelCodesOrNull - The channel codes for which to create image references. If null or empty, references for all channels will be created.
    wellsToUse - The wells to create image references for. Must not be null.
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)
                throws java.io.IOException
```
    Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams. Output streams will not be closed automatically.
    
    If there is an image reference specified which is not referring to the existing image on the server, nothing will be written to the output stream returned by the output streams provider. No exception will be thrown.
    The images will be converted to PNG format before being shipped.
    The number of image references has to be the same as the number of files.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.io.IOException - when reading images from the server or writing them to the output streams fails
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider,
              boolean convertToPNG)
                throws java.io.IOException
```
    Saves images for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams. Output streams will not be closed automatically.
    
    If there is an image reference specified which is not referring to the existing image on the server, nothing will be written to the output stream returned by the output streams provider. No exception will be thrown.
    If convertToPng==true, the images will be converted to PNG format before being shipped, otherwise they will be shipped in the format that they are stored on the server.
    The number of image references has to be the same as the number of files.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.io.IOException - when reading images from the server or writing them to the output streams fails
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              boolean convertToPNG,
              IPlateImageHandler plateImageHandler)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads images for a given list of image references (given by data set code, well position, channel and tile) and hands it over to the plateImageHandler.
    If convertToPng==true, the images will be converted to PNG format before being shipped, otherwise they will be shipped in the format that they are stored on the server.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - handles delivered images.
    
    Throws:
    
    java.io.IOException - when reading images from the server or writing them to the output streams fails
  - loadImages
```
public java.util.List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
                                java.util.List<WellPosition> wellPositions,
                                java.lang.String channel,
                                ImageSize thumbnailSizeOrNull)
                                  throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads original images or thumbnails for a specified data set, a list of well positions (empty list means all wells), a channel, and an optional thumb nail size. Images of all tiles are delivered. If thumb nail size isn't specified the original image is delivered otherwise a thumb nail image with same aspect ratio as the original image but which fits into specified size will be delivered.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    Returns:
    a list of byte arrays where each array contains a PNG encoded image.
    
    Throws:
    
    java.io.IOException
  - loadImages
```
public void loadImages(IDatasetIdentifier dataSetIdentifier,
              java.util.List<WellPosition> wellPositions,
              java.lang.String channel,
              ImageSize thumbnailSizeOrNull,
              IPlateImageHandler plateImageHandler)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads PNG-encoded images for specified data set, list of well positions (empty list means all wells), channel, and optional thumb nail size. Images of all tiles are delivered. If thumb nail size isn't specified the original image is delivered otherwise a thumb nail image with same aspect ratio as the original image but which fits into specified size will be delivered.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - handles delivered images.
    
    Throws:
    
    java.io.IOException
  - loadImageWellCaching
```
public byte[] loadImageWellCaching(PlateImageReference imageReference,
                          ImageSize imageSizeOrNull)
                            throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads an PNG-encoded image for the specified image reference and, optionally, image size. If the image size isn't specified, the original image is delivered, otherwise a scaled image with same aspect ratio as the original image but which fits into specified size will be delivered.
    
    Specified by:
    
    loadImageWellCaching in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.io.IOException
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              ImageSize sizeOrNull,
              IPlateImageHandler plateImageHandler)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads PNG-encoded images for specified image references and, optionally, image size. If the image size isn't specified, the original image is delivered, otherwise a scaled image with same aspect ratio as the original image but which fits into specified size will be delivered.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - handles delivered images.
    
    Throws:
    
    java.io.IOException
  - loadThumbnailImageWellCaching
```
public byte[] loadThumbnailImageWellCaching(PlateImageReference imageReference)
                                     throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads the PNG-encoded image for the specified imageReference.
    This method triggers loading the thumbnail images for all tiles and all channels for the given well and image data set. It is a method to be used in code that has to get one image at a time but eventually needs all images for a well and can increase performance of image loading considerably.
    
    Specified by:
    
    loadThumbnailImageWellCaching in interface IScreeningOpenbisServiceFacade
    
    Throws:
    
    java.io.IOException
  - loadThumbnailImages
```
public void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences,
                       IPlateImageHandler plateImageHandler)
                         throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams. Output streams will not be closed automatically.
    If no thumbnails are stored for this data set and well positions, empty images (length 0) will be returned.
    
    Specified by:
    
    loadThumbnailImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - Handles delivered images.
    
    Throws:
    
    java.io.IOException
  - loadThumbnailImages
```
public void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences,
                       ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)
                         throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads thumbnail images for specified data set, for a given list of image references (given by data set code, well position, channel and tile) in the provided output streams. Output streams will not be closed automatically.
    If no thumbnails are stored for this data set and well positions, empty images (length 0) will be returned.
    
    Specified by:
    
    loadThumbnailImages in interface IScreeningOpenbisServiceFacade
    
    outputStreamProvider - Handles delivered images.
    
    Throws:
    
    java.io.IOException
  - loadPhysicalThumbnails
```
public void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences,
                          ImageRepresentationFormat format,
                          IPlateImageHandler plateImageHandler)
                            throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Retrieves images for the specified image references and invokes the plateImageHandler passing in image data.
    If no images are stored for a particular combination of image reference and format, empty images (length 0) will be returned.
    
    Specified by:
    
    loadPhysicalThumbnails in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    imageReferences - The data set, well, channel, and tile of the image to be returned.
    format - The format of the image to return.
    plateImageHandler - Handles delivered images.
    
    Throws:
    
    java.io.IOException
  - loadPhysicalThumbnails
```
public void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences,
                          ImageRepresentationFormat format,
                          ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider)
                            throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Retrieves images for the specified image references and invokes the IImageOutputStreamProvider passing in image data.
    If no images are stored for a particular combination of image reference and format, empty images (length 0) will be returned.
    
    Specified by:
    
    loadPhysicalThumbnails in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    imageReferences - The data set, well, channel, and tile of the image to be returned.
    format - The format of the image to return.
    
    Throws:
    
    java.io.IOException
  - saveImageTransformerFactory
```
public void saveImageTransformerFactory(java.util.List<IDatasetIdentifier> dataSetIdentifiers,
                               java.lang.String channel,
                               ch.systemsx.cisd.base.image.IImageTransformerFactory transformerFactoryOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Saves the specified transformer factory for the specified channel and the experiment to which the specified data sets belong.
    
    Specified by:
    
    saveImageTransformerFactory in interface IScreeningOpenbisServiceFacade
  - getImageTransformerFactoryOrNull
```
public ch.systemsx.cisd.base.image.IImageTransformerFactory getImageTransformerFactoryOrNull(java.util.List<IDatasetIdentifier> dataSetIdentifiers,
                                                                                    java.lang.String channel)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns the transformer factory for the specified channel and the experiment to which the specified data sets belong.
    
    Specified by:
    
    getImageTransformerFactoryOrNull in interface IScreeningOpenbisServiceFacade
    
    Returns:
    null if such a factory has been defined yet.
  - listImageMetadata
```
public ImageDatasetMetadata listImageMetadata(IImageDatasetIdentifier imageDataset)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given image data set, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
    
    Specified by:
    
    listImageMetadata in interface IScreeningOpenbisServiceFacade
  - listImageMetadata
```
public java.util.List<ImageDatasetMetadata> listImageMetadata(java.util.List<? extends IImageDatasetIdentifier> imageDatasets)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given set of image data sets, provide meta like like which image channels have been acquired, what is the tile geometry, the available (natural) image size(s) and the like.
    
    Specified by:
    
    listImageMetadata in interface IScreeningOpenbisServiceFacade
  - listPlateMaterialMapping
```
public java.util.List<PlateWellMaterialMapping> listPlateMaterialMapping(java.util.List<? extends PlateIdentifier> plates,
                                                                MaterialTypeIdentifier materialTypeIdentifierOrNull)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    For a given list of plates, return the mapping of plate wells to materials contained in each well.
    
    Specified by:
    
    listPlateMaterialMapping in interface IScreeningOpenbisServiceFacade
    
    Parameters:
    plates - The list of plates to get the mapping for
    materialTypeIdentifierOrNull - If not null, consider only materials of the given type for the mapping.
    
    Returns:
    A list of well to material mappings, one element for each plate.
  - listAnalysisProcedures
```
public java.util.List<java.lang.String> listAnalysisProcedures(ExperimentIdentifier experimentIdentifier)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns an alphabetically sorted list of analysis procedure codes of all data sets of the specified experiment.
    
    Specified by:
    
    listAnalysisProcedures in interface IScreeningOpenbisServiceFacade
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              LoadImageConfiguration configuration,
              IPlateImageHandler plateImageHandler)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Loads images where the desired properties of the images are specified by a LoadImageConfiguration. The options and their behavior are described in the LoadImageConfiguration documentation.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    configuration - The configuration of the images to load.
    plateImageHandler - Handler for the delivered images.
    
    Throws:
    
    java.io.IOException
    See Also:
    LoadImageConfiguration
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              IPlateImageHandler plateImageHandler,
              ImageRepresentationFormat format)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and specified image representation format. The ImageRepresentationFormat argument should be an object returned by IScreeningOpenbisServiceFacade.listAvailableImageRepresentationFormats(List). This method assumes that all image references belong to the same data set which has image representations of specified format.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - Handler for the delivered images.
    
    Throws:
    
    java.io.IOException
  - loadImages
```
public void loadImages(java.util.List<PlateImageReference> imageReferences,
              IPlateImageHandler plateImageHandler,
              IImageRepresentationFormatSelectionCriterion... criteria)
                throws java.io.IOException
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Provides images for the specified list of image references (specified by data set code, well position, channel and tile) and image selection criteria. These criteria are applied to the ImageRepresentationFormat sets of each data set. Beside of the set of original images a data set can have other image representations like thumbnails of various sizes. The provided array of IImageRepresentationFormatSelectionCriterion are applied one after another onto the set of ImageRepresentationFormat until its size is reduced to one.
    
    Specified by:
    
    loadImages in interface IScreeningOpenbisServiceFacade
    
    plateImageHandler - Handler for the delivered images.
    
    Throws:
    
    java.io.IOException
  - getExperimentImageMetadata
```
public ExperimentImageMetadata getExperimentImageMetadata(ExperimentIdentifier experimentIdentifier)
```
    Description copied from interface: IScreeningOpenbisServiceFacade
    
    Returns aggregated metadata for all images/plates within one experiment.
    
    Specified by:
    
    getExperimentImageMetadata in interface IScreeningOpenbisServiceFacade
  - listAvailableImageRepresentationFormats
```
public java.util.List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(java.util.List<? extends IDatasetIdentifier> dataSetIdentifiers)
```
    Specified by:
    
    listAvailableImageRepresentationFormats in interface IScreeningOpenbisServiceFacade
    
    Returns:
    Information about the image representations available for the sepecified data sets.

Class ScreeningOpenbisServiceFacade

Nested Class Summary

Method Summary

Methods inherited from class java.lang.Object

Method Detail

tryCreate

tryCreate

tryCreateForTest

getSessionToken

logout

clearWellImageCache

listPlates

getPlateMetadataList

listPlates

listPlates

listExperiments

listExperiments

listFeatureVectorDatasets

listFeatureVectorDatasets

listImageDatasets

listRawImageDatasets

listSegmentationImageDatasets

listSegmentationImageDatasets

listPlateWells

listPlateWells

listPlateWells

getWellProperties

updateWellProperties

getDataSets

getDataSets

getDataSet

getDataSets

getDataSets

getFullDataSets

getDataSets

getFullDataSets

getDataSetMetaData

putDataSet

putDataSet

putDataSet

getDatasetIdentifiers

listAvailableFeatureNames

listAvailableFeatureCodes

getFeatureList

listAvailableFeatures

loadFeaturesForPlates

loadFeaturesForPlates

loadFeatures

convertToFeatureVectorDatasetWellIdentifier

loadFeaturesForDatasetWellReferences

loadFeaturesForPlateWells

loadFeaturesForPlateWells

loadFeaturesForPlateWells

loadFeaturesForPlateWells

convertToWellPositions

createPlateImageReferences

createPlateImageReferences

createPlateImageReferences

createPlateImageReferences

createPlateImageReferences

loadImages

loadImages

loadImages

loadImages

loadImages

loadImageWellCaching

loadImages

loadThumbnailImageWellCaching

loadThumbnailImages

loadThumbnailImages

loadPhysicalThumbnails

loadPhysicalThumbnails

saveImageTransformerFactory

getImageTransformerFactoryOrNull

listImageMetadata

listImageMetadata

listPlateMaterialMapping

listAnalysisProcedures

loadImages

loadImages