public class ScreeningOpenbisServiceFacade extends java.lang.Object implements IScreeningOpenbisServiceFacade
Modifier and Type | Class and Description |
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static interface |
ScreeningOpenbisServiceFacade.IImageOutputStreamProvider
An interface to provide mapping between image references and output streams where the images should be saved.
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Modifier and Type | Method and Description |
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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
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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.
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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.
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java.util.List<PlateImageReference> |
createPlateImageReferences(ImageDatasetReference imageDatasetRef)
Returns the list of all plate image references for the given imageDatasetRef.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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..
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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.
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ExperimentImageMetadata |
getExperimentImageMetadata(ExperimentIdentifier experimentIdentifier)
Returns aggregated metadata for all images/plates within one experiment.
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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
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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.
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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.
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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.
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java.util.List<PlateMetadata> |
getPlateMetadataList(java.util.List<? extends PlateIdentifier> plateIdentifiers)
Return full metadata for each specified plate, including wells and their properties.
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java.util.Map<java.lang.String,java.lang.String> |
getPlateProperties(PlateIdentifier plateIdentifier)
Returns all properties of specified plate as a map.
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java.lang.String |
getSessionToken()
Return the session token for this authenticated user.
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java.util.Map<java.lang.String,java.lang.String> |
getWellProperties(WellIdentifier wellIdentifier)
Returns all properties of specified well as a map.
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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.
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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.
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java.util.List<java.lang.String> |
listAvailableFeatureLists(IFeatureVectorDatasetIdentifier featureDataset)
For a given feature vector data set return a list of available feature lists.
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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.
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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.
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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).
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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).
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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.
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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.
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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.
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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.
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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.
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java.util.List<Plate> |
listPlates()
Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
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java.util.List<Plate> |
listPlates(ExperimentIdentifier experiment)
Return the list of all plates for the given experiment.
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java.util.List<Plate> |
listPlates(ExperimentIdentifier experiment,
java.lang.String analysisProcedure)
Return the list of all plates for the given experiment and analysis procedure.
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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.
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java.util.List<PlateWellReferenceWithDatasets> |
listPlateWells(MaterialIdentifier materialIdentifier,
boolean findDatasets)
For the given materialIdentifier find all plate locations that are connected to it.
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java.util.List<WellIdentifier> |
listPlateWells(PlateIdentifier plateIdentifier)
For the given plateIdentifier find all wells that are connected to it.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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byte[] |
loadImageWellCaching(PlateImageReference imageReference,
ImageSize imageSizeOrNull)
Loads an PNG-encoded image for the specified image reference and, optionally, image size.
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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.
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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.
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byte[] |
loadThumbnailImageWellCaching(PlateImageReference imageReference)
Loads the PNG-encoded image for the specified imageReference.
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void |
logout()
Closes connection with the server.
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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.
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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.
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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.
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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.
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java.util.List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material> |
searchForMaterials(ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria searchCriteria)
Searchs for Material given a search criteria.
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java.util.List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample> |
searchForSamples(ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria searchCriteria)
Searchs for Samples given a search criteria.
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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.
|
static IScreeningOpenbisServiceFacade |
tryCreateWithLocalDss(java.lang.String sessionToken,
java.lang.String serverUrl,
ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening localDss)
Creates a service facade which communicates with the openBIS server at the specified URL for an authenticated user.
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void |
updatePlateProperties(PlateIdentifier plateIdentifier,
java.util.Map<java.lang.String,java.lang.String> properties)
Updates properties of specified plate.
|
void |
updateWellProperties(WellIdentifier wellIdentifier,
java.util.Map<java.lang.String,java.lang.String> properties)
Updates properties of specified well.
|
public static IScreeningOpenbisServiceFacade tryCreate(java.lang.String userId, java.lang.String userPassword, java.lang.String serverUrl)
public static IScreeningOpenbisServiceFacade tryCreate(java.lang.String sessionToken, java.lang.String serverUrl)
sessionToken
- The session token for the authenticated userserverUrl
- The URL for the openBIS application serverpublic static IScreeningOpenbisServiceFacade tryCreateWithLocalDss(java.lang.String sessionToken, java.lang.String serverUrl, ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening localDss)
public static IScreeningOpenbisServiceFacade tryCreateForTest(java.lang.String sessionToken, java.lang.String serverUrl, ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer openbisServer)
public java.util.List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material> searchForMaterials(ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria searchCriteria)
searchForMaterials
in interface IScreeningOpenbisServiceFacade
public java.util.List<ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample> searchForSamples(ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria searchCriteria)
searchForSamples
in interface IScreeningOpenbisServiceFacade
public java.lang.String getSessionToken()
getSessionToken
in interface IScreeningOpenbisServiceFacade
public void logout()
logout
in interface IScreeningOpenbisServiceFacade
public void clearWellImageCache()
IScreeningOpenbisServiceFacade
IScreeningOpenbisServiceFacade.loadImageWellCaching(PlateImageReference, ImageSize)
and IScreeningOpenbisServiceFacade.loadThumbnailImageWellCaching(PlateImageReference)
from the image cache, thus
freeing the memory.clearWellImageCache
in interface IScreeningOpenbisServiceFacade
public java.util.List<Plate> listPlates()
listPlates
in interface IScreeningOpenbisServiceFacade
public java.util.List<PlateMetadata> getPlateMetadataList(java.util.List<? extends PlateIdentifier> plateIdentifiers)
IScreeningOpenbisServiceFacade
getPlateMetadataList
in interface IScreeningOpenbisServiceFacade
public java.util.List<Plate> listPlates(ExperimentIdentifier experiment)
listPlates
in interface IScreeningOpenbisServiceFacade
public java.util.List<Plate> listPlates(ExperimentIdentifier experiment, java.lang.String analysisProcedure)
IScreeningOpenbisServiceFacade
listPlates
in interface IScreeningOpenbisServiceFacade
public java.util.List<ExperimentIdentifier> listExperiments()
IScreeningOpenbisServiceFacade
listExperiments
in interface IScreeningOpenbisServiceFacade
public java.util.List<ExperimentIdentifier> listExperiments(java.lang.String userId)
IScreeningOpenbisServiceFacade
The user calling this method needs to have a role INSTANCE_OBSERVER
on the
openBIS instance.
listExperiments
in interface IScreeningOpenbisServiceFacade
public java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates)
listFeatureVectorDatasets
in interface IScreeningOpenbisServiceFacade
public java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)
IScreeningOpenbisServiceFacade
listFeatureVectorDatasets
in interface IScreeningOpenbisServiceFacade
analysisProcedureOrNull
- If null
returned list isn't filtered on analysis
procedure property.@Deprecated public java.util.List<ImageDatasetReference> listImageDatasets(java.util.List<? extends PlateIdentifier> plates)
listRawImageDatasets(List)
instead.listImageDatasets
in interface IScreeningOpenbisServiceFacade
public java.util.List<ImageDatasetReference> listRawImageDatasets(java.util.List<? extends PlateIdentifier> plates)
listRawImageDatasets
in interface IScreeningOpenbisServiceFacade
public java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates)
listSegmentationImageDatasets
in interface IScreeningOpenbisServiceFacade
public java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)
IScreeningOpenbisServiceFacade
listSegmentationImageDatasets
in interface IScreeningOpenbisServiceFacade
analysisProcedureOrNull
- If null
no restriction applies.public java.util.List<PlateWellReferenceWithDatasets> listPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, boolean findDatasets)
findDatasets == true
, find also the connected image and image analysis data sets for the relevant plates.listPlateWells
in interface IScreeningOpenbisServiceFacade
public java.util.List<PlateWellReferenceWithDatasets> listPlateWells(MaterialIdentifier materialIdentifier, boolean findDatasets)
findDatasets == true
, find also
the connected image and image analysis data sets for the relevant plates.listPlateWells
in interface IScreeningOpenbisServiceFacade
public java.util.List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier)
listPlateWells
in interface IScreeningOpenbisServiceFacade
public java.util.Map<java.lang.String,java.lang.String> getPlateProperties(PlateIdentifier plateIdentifier)
IScreeningOpenbisServiceFacade
getPlateProperties
in interface IScreeningOpenbisServiceFacade
public void updatePlateProperties(PlateIdentifier plateIdentifier, java.util.Map<java.lang.String,java.lang.String> properties)
IScreeningOpenbisServiceFacade
updatePlateProperties
in interface IScreeningOpenbisServiceFacade
public java.util.Map<java.lang.String,java.lang.String> getWellProperties(WellIdentifier wellIdentifier)
IScreeningOpenbisServiceFacade
getWellProperties
in interface IScreeningOpenbisServiceFacade
public void updateWellProperties(WellIdentifier wellIdentifier, java.util.Map<java.lang.String,java.lang.String> properties)
IScreeningOpenbisServiceFacade
updateWellProperties
in interface IScreeningOpenbisServiceFacade
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
getDataSets
in interface IScreeningOpenbisServiceFacade
datasetTypeCodePattern
- only datasets of the type which matche the specified pattern
will be returned. To fetch all datasets specify ".*".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.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
IScreeningOpenbisServiceFacade
getDataSets
in interface IScreeningOpenbisServiceFacade
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.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
getDataSet
in interface IScreeningOpenbisServiceFacade
java.lang.IllegalStateException
ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
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
getDataSets
in interface IScreeningOpenbisServiceFacade
datasetTypeCodePattern
- only datasets of the type which matche the specified pattern
will be returned. To fetch all datasets specify ".*".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.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
IScreeningOpenbisServiceFacade
getDataSets
in interface IScreeningOpenbisServiceFacade
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.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
IScreeningOpenbisServiceFacade
getFullDataSets
in interface IScreeningOpenbisServiceFacade
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.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)
IScreeningOpenbisServiceFacade
getDataSets
in interface IScreeningOpenbisServiceFacade
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
IScreeningOpenbisServiceFacade
getFullDataSets
in interface IScreeningOpenbisServiceFacade
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.public java.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getDataSetMetaData(java.util.List<java.lang.String> dataSetCodes)
IScreeningOpenbisServiceFacade
getDataSetMetaData
in interface IScreeningOpenbisServiceFacade
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
putDataSet
in interface IScreeningOpenbisServiceFacade
wellIdentifier
- Identifier of a well that should become owner of the new data setdataSetFile
- A file or folder containing the datadataSetMetadataOrNull
- The optional metadata overriding server defaults for the new data setjava.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 failspublic 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
IScreeningOpenbisServiceFacade
putDataSet
in interface IScreeningOpenbisServiceFacade
plateIdentifier
- Identifier of a plate that should become owner of the new data setdataSetFile
- A file or folder containing the datadataSetMetadataOrNull
- The optional metadata overriding server defaults for the new
data setjava.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 failspublic 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
IScreeningOpenbisServiceFacade
putDataSet
in interface IScreeningOpenbisServiceFacade
experimentIdentifier
- Identifier of a experiment that should become owner of the new
data setdataSetFile
- A file or folder containing the datadataSetMetadataOrNull
- The optional metadata overriding server defaults for the new
data setjava.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 failspublic java.util.List<IDatasetIdentifier> getDatasetIdentifiers(java.util.List<java.lang.String> datasetCodes)
getDatasetIdentifiers
in interface IScreeningOpenbisServiceFacade
public java.util.List<java.lang.String> listAvailableFeatureNames(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
IScreeningOpenbisServiceFacade
listAvailableFeatureNames
in interface IScreeningOpenbisServiceFacade
public java.util.List<java.lang.String> listAvailableFeatureCodes(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
listAvailableFeatureCodes
in interface IScreeningOpenbisServiceFacade
public java.util.List<java.lang.String> listAvailableFeatureLists(IFeatureVectorDatasetIdentifier featureDataset)
IScreeningOpenbisServiceFacade
listAvailableFeatureLists
in interface IScreeningOpenbisServiceFacade
public java.util.List<java.lang.String> getFeatureList(IFeatureVectorDatasetIdentifier featureDataset, java.lang.String featureListCode)
IScreeningOpenbisServiceFacade
getFeatureList
in interface IScreeningOpenbisServiceFacade
public java.util.List<FeatureInformation> listAvailableFeatures(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
listAvailableFeatures
in interface IScreeningOpenbisServiceFacade
public java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull)
loadFeaturesForPlates
in interface IScreeningOpenbisServiceFacade
plates
- The plates to get the feature vectors forfeatureCodesOrNull
- The codes of the features to load, or null
, if all available features should be loaded.FeatureVectorDataset
s, each element corresponds to one of the featureDatasets.public java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull, java.lang.String analysisProcedureOrNull)
IScreeningOpenbisServiceFacade
loadFeaturesForPlates
in interface IScreeningOpenbisServiceFacade
plates
- The plates to get the feature vectors forfeatureCodesOrNull
- 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.FeatureVectorDataset
s, each element corresponds to one of the
featureDatasets.public java.util.List<FeatureVectorDataset> loadFeatures(java.util.List<FeatureVectorDatasetReference> featureDatasets, java.util.List<java.lang.String> featureCodesOrNull)
loadFeatures
in interface IScreeningOpenbisServiceFacade
featureDatasets
- The data sets to get the feature vectors forfeatureCodesOrNull
- The codes of the features to load, or null
, if all available features should be loaded.FeatureVectorDataset
s, each element corresponds to one of the featureDatasets.public java.util.List<FeatureVectorDatasetWellReference> convertToFeatureVectorDatasetWellIdentifier(java.util.List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets)
IScreeningOpenbisServiceFacade
PlateWellReferenceWithDatasets
into a list of
FeatureVectorDatasetWellReference
.public java.util.List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences, java.util.List<java.lang.String> featureCodesOrNull)
IScreeningOpenbisServiceFacade
Physically, the result is delivered as a list of feature vectors. Each entry in this list corresponds to one well in one dataset.
loadFeaturesForDatasetWellReferences
in interface IScreeningOpenbisServiceFacade
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.FeatureVectorWithDescription
s, 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.public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)
IScreeningOpenbisServiceFacade
null
, or all available features otherwise.loadFeaturesForPlateWells
in interface IScreeningOpenbisServiceFacade
experimentIdentifer
- The identifier of the experiment to get the feature vectors formaterialIdentifier
- 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.FeatureVectorWithDescription
s found in the given
experimentIdentifer and connected with the given
materialIdentifier.public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)
IScreeningOpenbisServiceFacade
null
, or all available features otherwise. Do this only for
data sets with specified value of property ANALYSIS_PROCEDURE
, if not
null
.loadFeaturesForPlateWells
in interface IScreeningOpenbisServiceFacade
experimentIdentifer
- The identifier of the experiment to get the feature vectors formaterialIdentifier
- 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.FeatureVectorWithDescription
s found in the given
experimentIdentifer and connected with the given
materialIdentifier.public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)
IScreeningOpenbisServiceFacade
null
, or all
available features otherwise.loadFeaturesForPlateWells
in interface IScreeningOpenbisServiceFacade
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.FeatureVectorWithDescription
s found in the given
experimentIdentifer and connected with the given
materialIdentifier.public java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)
IScreeningOpenbisServiceFacade
null
, or all
available features otherwise. Do this only for data sets with specified value of property
ANALYSIS_PROCEDURE
, if not null
.loadFeaturesForPlateWells
in interface IScreeningOpenbisServiceFacade
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.FeatureVectorWithDescription
s found in the given
experimentIdentifer and connected with the given
materialIdentifier.public java.util.List<WellPosition> convertToWellPositions(java.util.List<WellIdentifier> wellIds)
IScreeningOpenbisServiceFacade
convertToWellPositions
in interface IScreeningOpenbisServiceFacade
public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef)
IScreeningOpenbisServiceFacade
createPlateImageReferences
in interface IScreeningOpenbisServiceFacade
public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)
IScreeningOpenbisServiceFacade
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.public java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)
IScreeningOpenbisServiceFacade
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.public java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetId, java.util.List<java.lang.String> channeldCodesOrNull, java.util.List<WellPosition> wellsToUse)
IScreeningOpenbisServiceFacade
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
.public java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetId, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsToUse)
IScreeningOpenbisServiceFacade
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
.public void loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
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.loadImages
in interface IScreeningOpenbisServiceFacade
java.io.IOException
- when reading images from the server or writing them to the output streams failspublic void loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider, boolean convertToPNG) throws java.io.IOException
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.
IfconvertToPng==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.loadImages
in interface IScreeningOpenbisServiceFacade
java.io.IOException
- when reading images from the server or writing them to the output streams failspublic void loadImages(java.util.List<PlateImageReference> imageReferences, boolean convertToPNG, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
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.loadImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- handles delivered images.java.io.IOException
- when reading images from the server or writing them to the output streams
failspublic java.util.List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadImages
in interface IScreeningOpenbisServiceFacade
java.io.IOException
public void loadImages(IDatasetIdentifier dataSetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- handles delivered images.java.io.IOException
public byte[] loadImageWellCaching(PlateImageReference imageReference, ImageSize imageSizeOrNull) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadImageWellCaching
in interface IScreeningOpenbisServiceFacade
java.io.IOException
public void loadImages(java.util.List<PlateImageReference> imageReferences, ImageSize sizeOrNull, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- handles delivered images.java.io.IOException
public byte[] loadThumbnailImageWellCaching(PlateImageReference imageReference) throws java.io.IOException
IScreeningOpenbisServiceFacade
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.
loadThumbnailImageWellCaching
in interface IScreeningOpenbisServiceFacade
java.io.IOException
public void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadThumbnailImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- Handles delivered images.java.io.IOException
public void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadThumbnailImages
in interface IScreeningOpenbisServiceFacade
outputStreamProvider
- Handles delivered images.java.io.IOException
public void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadPhysicalThumbnails
in interface IScreeningOpenbisServiceFacade
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.java.io.IOException
public void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
IScreeningOpenbisServiceFacade
loadPhysicalThumbnails
in interface IScreeningOpenbisServiceFacade
imageReferences
- The data set, well, channel, and tile of the image to be returned.format
- The format of the image to return.java.io.IOException
public void saveImageTransformerFactory(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel, ch.systemsx.cisd.base.image.IImageTransformerFactory transformerFactoryOrNull)
IScreeningOpenbisServiceFacade
saveImageTransformerFactory
in interface IScreeningOpenbisServiceFacade
public ch.systemsx.cisd.base.image.IImageTransformerFactory getImageTransformerFactoryOrNull(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel)
IScreeningOpenbisServiceFacade
getImageTransformerFactoryOrNull
in interface IScreeningOpenbisServiceFacade
null
if such a factory has been defined yet.public ImageDatasetMetadata listImageMetadata(IImageDatasetIdentifier imageDataset)
IScreeningOpenbisServiceFacade
listImageMetadata
in interface IScreeningOpenbisServiceFacade
public java.util.List<ImageDatasetMetadata> listImageMetadata(java.util.List<? extends IImageDatasetIdentifier> imageDatasets)
IScreeningOpenbisServiceFacade
listImageMetadata
in interface IScreeningOpenbisServiceFacade
public java.util.List<PlateWellMaterialMapping> listPlateMaterialMapping(java.util.List<? extends PlateIdentifier> plates, MaterialTypeIdentifier materialTypeIdentifierOrNull)
IScreeningOpenbisServiceFacade
listPlateMaterialMapping
in interface IScreeningOpenbisServiceFacade
plates
- The list of plates to get the mapping formaterialTypeIdentifierOrNull
- If not null
, consider only materials of the
given type for the mapping.public java.util.List<java.lang.String> listAnalysisProcedures(ExperimentIdentifier experimentIdentifier)
IScreeningOpenbisServiceFacade
listAnalysisProcedures
in interface IScreeningOpenbisServiceFacade
public void loadImages(java.util.List<PlateImageReference> imageReferences, LoadImageConfiguration configuration, IPlateImageHandler plateImageHandler) throws java.io.IOException
IScreeningOpenbisServiceFacade
LoadImageConfiguration
documentation.loadImages
in interface IScreeningOpenbisServiceFacade
configuration
- The configuration of the images to load.plateImageHandler
- Handler for the delivered images.java.io.IOException
LoadImageConfiguration
public void loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, ImageRepresentationFormat format) throws java.io.IOException
IScreeningOpenbisServiceFacade
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.loadImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- Handler for the delivered images.java.io.IOException
public void loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, IImageRepresentationFormatSelectionCriterion... criteria) throws java.io.IOException
IScreeningOpenbisServiceFacade
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.loadImages
in interface IScreeningOpenbisServiceFacade
plateImageHandler
- Handler for the delivered images.java.io.IOException
public ExperimentImageMetadata getExperimentImageMetadata(ExperimentIdentifier experimentIdentifier)
IScreeningOpenbisServiceFacade
getExperimentImageMetadata
in interface IScreeningOpenbisServiceFacade
public java.util.List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(java.util.List<? extends IDatasetIdentifier> dataSetIdentifiers)
listAvailableImageRepresentationFormats
in interface IScreeningOpenbisServiceFacade