public interface IScreeningOpenbisServiceFacade
Modifier and Type | Method and Description |
---|---|
void |
clearWellImageCache()
Removes all images loaded by
loadImageWellCaching(PlateImageReference, ImageSize)
and 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 imageDatasetRef,
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 imageDatasetRef,
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(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 plateIdentifier,
ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter)
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)
Deprecated.
use
getDataSets(PlateIdentifier, IDataSetFilter) with
TypeBasedDataSetFilter . |
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)
Deprecated.
use
getDataSets(WellIdentifier, IDataSetFilter) with
TypeBasedDataSetFilter . |
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.util.Map<java.lang.String,java.lang.String> |
getPlateProperties(PlateIdentifier plateIdentifier)
Returns all properties of specified plate as a map.
|
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> |
listAvailableFeatureLists(IFeatureVectorDatasetIdentifier featureDataset)
For a given feature vector data set return a list of available feature lists.
|
java.util.List<java.lang.String> |
listAvailableFeatureNames(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
Deprecated.
Use
listAvailableFeatureCodes(List) instead. Since version 1.2 of the
API features are no longer identified by a name but by a code. Previous client
code still works but the name will be normalized internally. "Normalized" means
that the original name argument is converted to upper case and any symbol which
isn't from A-Z or 0-9 is replaced by an underscore character. The
FeatureVectorDataset will provide feature codes and feature labels. |
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
segmentation images (overlays).
|
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)
Deprecated.
use
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, String, List)
with third argument set to null . |
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)
Deprecated.
use
loadFeaturesForPlateWells(MaterialIdentifier, String, List) with
second argument set to null . |
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 imageSizeOrNull,
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.
|
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)
Exposes material search functionaliy (used for ScreeningML)
|
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)
Exposes material search functionaliy (used for ScreeningML)
|
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.
|
java.lang.String getSessionToken()
void logout()
void clearWellImageCache()
loadImageWellCaching(PlateImageReference, ImageSize)
and loadThumbnailImageWellCaching(PlateImageReference)
from the image cache, thus
freeing the memory.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)
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)
java.util.List<Plate> listPlates()
java.util.List<PlateMetadata> getPlateMetadataList(java.util.List<? extends PlateIdentifier> plateIdentifiers)
java.util.List<Plate> listPlates(ExperimentIdentifier experiment)
java.util.List<Plate> listPlates(ExperimentIdentifier experiment, java.lang.String analysisProcedure)
java.util.List<ExperimentIdentifier> listExperiments()
java.util.List<ExperimentIdentifier> listExperiments(java.lang.String userId)
The user calling this method needs to have a role INSTANCE_OBSERVER
on the
openBIS instance.
java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates)
java.util.List<FeatureVectorDatasetReference> listFeatureVectorDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)
analysisProcedureOrNull
- If null
returned list isn't filtered on analysis
procedure property.@Deprecated java.util.List<ImageDatasetReference> listImageDatasets(java.util.List<? extends PlateIdentifier> plates)
listRawImageDatasets(List)
instead.java.util.List<ImageDatasetReference> listRawImageDatasets(java.util.List<? extends PlateIdentifier> plates)
java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates)
java.util.List<ImageDatasetReference> listSegmentationImageDatasets(java.util.List<? extends PlateIdentifier> plates, java.lang.String analysisProcedureOrNull)
analysisProcedureOrNull
- If null
no restriction applies.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.
For how to get the feature vectors, see
convertToFeatureVectorDatasetWellIdentifier(List)
.
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.java.util.List<WellIdentifier> listPlateWells(PlateIdentifier plateIdentifier)
java.util.Map<java.lang.String,java.lang.String> getPlateProperties(PlateIdentifier plateIdentifier)
void updatePlateProperties(PlateIdentifier plateIdentifier, java.util.Map<java.lang.String,java.lang.String> properties)
java.util.Map<java.lang.String,java.lang.String> getWellProperties(WellIdentifier wellIdentifier)
void updateWellProperties(WellIdentifier wellIdentifier, java.util.Map<java.lang.String,java.lang.String> properties)
@Deprecated 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(WellIdentifier, IDataSetFilter)
with
TypeBasedDataSetFilter
.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.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
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.ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss getDataSet(java.lang.String dataSetCode) throws java.lang.IllegalStateException, ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
java.lang.IllegalStateException
ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
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
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 fails@Deprecated 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(PlateIdentifier, IDataSetFilter)
with
TypeBasedDataSetFilter
.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.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
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.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
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.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss> getDataSets(ExperimentIdentifier plateIdentifier, ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter dataSetFilter) throws java.lang.IllegalStateException, ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
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.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
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.util.List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getDataSetMetaData(java.util.List<java.lang.String> dataSetCodes) throws java.lang.IllegalStateException, ch.systemsx.cisd.common.exceptions.EnvironmentFailureException
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.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
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 failsch.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
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 failsjava.util.List<FeatureVectorDatasetWellReference> convertToFeatureVectorDatasetWellIdentifier(java.util.List<PlateWellReferenceWithDatasets> plateWellReferenceWithDataSets)
PlateWellReferenceWithDatasets
into a list of
FeatureVectorDatasetWellReference
.java.util.List<IDatasetIdentifier> getDatasetIdentifiers(java.util.List<java.lang.String> datasetCodes)
@Deprecated java.util.List<java.lang.String> listAvailableFeatureNames(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
listAvailableFeatureCodes(List)
instead. Since version 1.2 of the
API features are no longer identified by a name but by a code. Previous client
code still works but the name will be normalized internally. "Normalized" means
that the original name argument is converted to upper case and any symbol which
isn't from A-Z or 0-9 is replaced by an underscore character. The
FeatureVectorDataset
will provide feature codes and feature labels.java.util.List<java.lang.String> listAvailableFeatureCodes(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
java.util.List<FeatureInformation> listAvailableFeatures(java.util.List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
java.util.List<java.lang.String> listAvailableFeatureLists(IFeatureVectorDatasetIdentifier featureDataset)
java.util.List<java.lang.String> getFeatureList(IFeatureVectorDatasetIdentifier featureDataset, java.lang.String featureListCode)
java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull)
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.java.util.List<FeatureVectorDataset> loadFeaturesForPlates(java.util.List<? extends PlateIdentifier> plates, java.util.List<java.lang.String> featureCodesOrNull, java.lang.String analysisProcedureOrNull)
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.java.util.List<FeatureVectorDataset> loadFeatures(java.util.List<FeatureVectorDatasetReference> featureDatasets, java.util.List<java.lang.String> featureCodesOrNull)
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.java.util.List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(java.util.List<FeatureVectorDatasetWellReference> datasetWellReferences, java.util.List<java.lang.String> featureCodesOrNull)
Physically, the result is delivered as a list of feature vectors. Each entry in this list corresponds to one well in one dataset.
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.@Deprecated java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)
loadFeaturesForPlateWells(ExperimentIdentifier, MaterialIdentifier, String, List)
with third argument set to null
.null
, or all available features otherwise.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.java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)
null
, or all available features otherwise. Do this only for
data sets with specified value of property ANALYSIS_PROCEDURE
, if not
null
.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.@Deprecated java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.util.List<java.lang.String> featureCodesOrNull)
loadFeaturesForPlateWells(MaterialIdentifier, String, List)
with
second argument set to null
.null
, or all
available features otherwise.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.java.util.List<FeatureVectorWithDescription> loadFeaturesForPlateWells(MaterialIdentifier materialIdentifier, java.lang.String analysisProcedureOrNull, java.util.List<java.lang.String> featureCodesOrNull)
null
, or all
available features otherwise. Do this only for data sets with specified value of property
ANALYSIS_PROCEDURE
, if not null
.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.java.util.List<WellPosition> convertToWellPositions(java.util.List<WellIdentifier> wellIds)
java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef)
java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)
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.java.util.List<PlateImageReference> createPlateImageReferences(ImageDatasetReference imageDatasetRef, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsOrNull)
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.java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetRef, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsToUse)
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
.java.util.List<PlateImageReference> createPlateImageReferences(IImageDatasetIdentifier imageDatasetRef, ImageDatasetMetadata metadataOrNull, java.util.List<java.lang.String> channelCodesOrNull, java.util.List<WellPosition> wellsToUse)
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
.void loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
java.io.IOException
- when reading images from the server or writing them to the output streams
failsvoid loadImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider, boolean convertToPNG) throws java.io.IOException
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.java.io.IOException
- when reading images from the server or writing them to the output streams
failsvoid loadImages(java.util.List<PlateImageReference> imageReferences, boolean convertToPNG, IPlateImageHandler plateImageHandler) throws java.io.IOException
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.plateImageHandler
- handles delivered images.java.io.IOException
- when reading images from the server or writing them to the output streams
failsjava.util.List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull) throws java.io.IOException
java.io.IOException
void loadImages(IDatasetIdentifier datasetIdentifier, java.util.List<WellPosition> wellPositions, java.lang.String channel, ImageSize thumbnailSizeOrNull, IPlateImageHandler plateImageHandler) throws java.io.IOException
plateImageHandler
- handles delivered images.java.io.IOException
byte[] loadImageWellCaching(PlateImageReference imageReference, ImageSize imageSizeOrNull) throws java.io.IOException
java.io.IOException
void loadImages(java.util.List<PlateImageReference> imageReferences, ImageSize imageSizeOrNull, IPlateImageHandler plateImageHandler) throws java.io.IOException
plateImageHandler
- handles delivered images.java.io.IOException
void loadImages(java.util.List<PlateImageReference> imageReferences, LoadImageConfiguration configuration, IPlateImageHandler plateImageHandler) throws java.io.IOException
LoadImageConfiguration
documentation.configuration
- The configuration of the images to load.plateImageHandler
- Handler for the delivered images.java.io.IOException
LoadImageConfiguration
void loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, ImageRepresentationFormat format) throws java.io.IOException
ImageRepresentationFormat
argument should be an object returned by
listAvailableImageRepresentationFormats(List)
. This method assumes that all image
references belong to the same data set which has image representations of specified format.plateImageHandler
- Handler for the delivered images.ch.systemsx.cisd.common.exceptions.UserFailureException
- if the specified format refers to an image representations
unknown by at least one plate image reference.java.io.IOException
void loadImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler, IImageRepresentationFormatSelectionCriterion... criteria) throws java.io.IOException
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.plateImageHandler
- Handler for the delivered images.ch.systemsx.cisd.common.exceptions.UserFailureException
- if no criterion has been specified (i.e. criteria
is an empty array) or if for at least one data set the filtered
ImageRepresentationFormat
set has size zero or greater than one.java.io.IOException
byte[] loadThumbnailImageWellCaching(PlateImageReference imageReference) throws java.io.IOException
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.
java.io.IOException
void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, IPlateImageHandler plateImageHandler) throws java.io.IOException
plateImageHandler
- Handles delivered images.java.io.IOException
void loadThumbnailImages(java.util.List<PlateImageReference> imageReferences, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
outputStreamProvider
- Handles delivered images.java.io.IOException
void saveImageTransformerFactory(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel, ch.systemsx.cisd.base.image.IImageTransformerFactory transformerFactoryOrNull)
ch.systemsx.cisd.base.image.IImageTransformerFactory getImageTransformerFactoryOrNull(java.util.List<IDatasetIdentifier> dataSetIdentifiers, java.lang.String channel)
null
if such a factory has been defined yet.ImageDatasetMetadata listImageMetadata(IImageDatasetIdentifier imageDataset)
java.util.List<ImageDatasetMetadata> listImageMetadata(java.util.List<? extends IImageDatasetIdentifier> imageDatasets)
java.util.List<PlateWellMaterialMapping> listPlateMaterialMapping(java.util.List<? extends PlateIdentifier> plates, MaterialTypeIdentifier materialTypeIdentifierOrNull)
plates
- The list of plates to get the mapping formaterialTypeIdentifierOrNull
- If not null
, consider only materials of the
given type for the mapping.java.util.List<java.lang.String> listAnalysisProcedures(ExperimentIdentifier experimentIdentifier)
ExperimentImageMetadata getExperimentImageMetadata(ExperimentIdentifier experimentIdentifier)
java.util.List<DatasetImageRepresentationFormats> listAvailableImageRepresentationFormats(java.util.List<? extends IDatasetIdentifier> dataSetIdentifiers)
void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, IPlateImageHandler plateImageHandler) throws java.io.IOException
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
void loadPhysicalThumbnails(java.util.List<PlateImageReference> imageReferences, ImageRepresentationFormat format, ScreeningOpenbisServiceFacade.IImageOutputStreamProvider outputStreamProvider) throws java.io.IOException
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