Package ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl

Class ImageContainerDataSet

java.lang.Object

ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.impl.ImageContainerDataSet

All Implemented Interfaces:

IDataSet, IDataSetUpdatable, IImageDataSet, IDataSetImmutable, IMetaprojectContent

public class ImageContainerDataSet
extends DataSet<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>
implements IImageDataSet

Represents an image data set for the registration API.

Field Summary

Fields

Modifier and Type	Field	Description
protected ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedBasicOpenBISService	service

Constructor Summary

Constructors

Constructor	Description
ImageContainerDataSet(DataSetRegistrationDetails<? extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation> registrationDetails, java.io.File dataSetFolder, ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService service)

Method Summary

Modifier and Type	Method	Description
void	establishSampleLinkForContainedDataSets()	If this method is called the contained data sets (original data set and thumbnails) will automatically linked to the sample specified by IDataSetUpdatable.setSample(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable) .
java.lang.String	figureGeometry()	Utility method to find out the plate geometry by looking for which wells images are available.
protected DataSetType	getDataSetTypeWithPropertyTypes(java.lang.String dataSetTypeCode)
DataSet<ImageDataSetInformation>	getOriginalDataset()
java.util.List<IDataSet>	getThumbnailDatasets()
boolean	sampleLinkForContainedDataSetsShouldBeEstablished()
void	setAnalysisProcedure(java.lang.String analysisProcedure)	Sets analysis procedure.
void	setExperiment(IExperimentImmutable experimentOrNull)	Set the experiment for this data set.
void	setOriginalDataset(DataSet<ImageDataSetInformation> originalDataset)
void	setSample(ISampleImmutable sampleOrNull)	Set the sample for this data set.
void	setThumbnailDatasets(java.util.List<IDataSet> thumbnailDatasets)

Methods inherited from class ch.systemsx.cisd.etlserver.registrator.api.v2.impl.DataSet

getAllPropertyCodes, getChildrenDataSets, getContainedDataSetCodes, getContainerDataSet, getContainerDataSets, getDataSetCode, getDataSetKind, getDataSetStagingFolder, getDataSetType, getDataSetTypeWithPropertyTypes, getEntityId, getExperiment, getExternalCode, getExternalDataManagementSystem, getFileFormatType, getOrderInContainer, getParentDatasets, getPropertyValue, getRegistrationDetails, getSample, getSpeedHint, isContainedDataSet, isContainerDataSet, isLinkDataSet, isMeasuredData, isNoFileDataSet, isPostRegistered, setContainedDataSetCodes, setDataSetKind, setDataSetType, setExperiment, setExternalCode, setExternalDataManagementSystem, setFileFormatType, setMeasuredData, setParentDatasets, setPropertyValue, setSpeedHint, tryDataSetContents

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet

setDataSetKind, setDataSetType, setMeasuredData, setSpeedHint

Methods inherited from interface ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable

getAllPropertyCodes, getChildrenDataSets, getContainedDataSetCodes, getContainerDataSet, getContainerDataSets, getDataSetCode, getDataSetKind, getDataSetType, getDataSetTypeWithPropertyTypes, getExperiment, getExternalCode, getExternalDataManagementSystem, getFileFormatType, getOrderInContainer, getParentDatasets, getPropertyValue, getSample, getSpeedHint, isContainedDataSet, isContainerDataSet, isLinkDataSet, isMeasuredData, isNoFileDataSet, isPostRegistered

Methods inherited from interface ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable

setContainedDataSetCodes, setExternalCode, setExternalDataManagementSystem, setFileFormatType, setParentDatasets, setPropertyValue

Methods inherited from interface ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMetaprojectContent

getEntityId

Field Detail

service

protected final ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedBasicOpenBISService service

Constructor Detail

ImageContainerDataSet

public ImageContainerDataSet(DataSetRegistrationDetails<? extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation> registrationDetails,
                             java.io.File dataSetFolder,
                             ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService service)

Method Detail

setAnalysisProcedure

public void setAnalysisProcedure(java.lang.String analysisProcedure)

Description copied from interface: IImageDataSet

Sets analysis procedure. Makes sense only for segmentation datasets.

Specified by:

setAnalysisProcedure in interface IImageDataSet

establishSampleLinkForContainedDataSets

public void establishSampleLinkForContainedDataSets()

Description copied from interface: IImageDataSet

If this method is called the contained data sets (original data set and thumbnails) will automatically linked to the sample specified by IDataSetUpdatable.setSample(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable) . By default there will be no such links.

Specified by:

establishSampleLinkForContainedDataSets in interface IImageDataSet

sampleLinkForContainedDataSetsShouldBeEstablished

public boolean sampleLinkForContainedDataSetsShouldBeEstablished()

getOriginalDataset

public DataSet<ImageDataSetInformation> getOriginalDataset()

Specified by:

getOriginalDataset in interface IImageDataSet

setOriginalDataset

public void setOriginalDataset(DataSet<ImageDataSetInformation> originalDataset)

getThumbnailDatasets

public java.util.List<IDataSet> getThumbnailDatasets()

Specified by:

getThumbnailDatasets in interface IImageDataSet

setThumbnailDatasets

public void setThumbnailDatasets(java.util.List<IDataSet> thumbnailDatasets)

setSample

public void setSample(ISampleImmutable sampleOrNull)

Description copied from interface: IDataSetUpdatable

Set the sample for this data set. Will also set the experiment, since the sample must have an experiment.

Specified by:

setSample in interface IDataSetUpdatable

Overrides:

setSample in class DataSet<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

Parameters:

sampleOrNull - The sample to use. Need not actually be immutable, but the immutable one is the supertype.

setExperiment

public void setExperiment(IExperimentImmutable experimentOrNull)

Description copied from interface: IDataSetUpdatable

Set the experiment for this data set. The experiment may also be set by setting the sample.

Specified by:

setExperiment in interface IDataSetUpdatable

Overrides:

setExperiment in class DataSet<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

Parameters:

experimentOrNull - The experiment for this data set. Need not actually be immutable, but the immutable one is the supertype.

figureGeometry

public java.lang.String figureGeometry()

Description copied from interface: IImageDataSet

Utility method to find out the plate geometry by looking for which wells images are available.

Specified by:

figureGeometry in interface IImageDataSet

Returns:

a constant which can be used as a vocabulary term value for $PLATE_GEOMETRY property of a plate/

getDataSetTypeWithPropertyTypes

protected DataSetType getDataSetTypeWithPropertyTypes(java.lang.String dataSetTypeCode)