Package fr.igred.omero.repository

Class DatasetWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.repository.GenericRepositoryObjectWrapper<DatasetData>

fr.igred.omero.repository.DatasetWrapper

public class DatasetWrapper
extends GenericRepositoryObjectWrapper<DatasetData>

Class containing a DatasetData.

Implements function using the DatasetData contained

Nested Class Summary

Nested classes/interfaces inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

GenericRepositoryObjectWrapper.ReplacePolicy

Field Summary

Fields

Modifier and Type	Field	Description
static String	ANNOTATION_LINK

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

Constructor	Description
DatasetWrapper(String name, String description)	Constructor of the DatasetWrapper class
DatasetWrapper(DatasetData dataset)	Constructor of the DatasetWrapper class

Method Summary

Modifier and Type	Method	Description
void	addImage(Client client, ImageWrapper image)	Adds a single image to the dataset in OMERO
void	addImages(Client client, List<? extends ImageWrapper> images)	Adds a list of image to the dataset in OMERO.
protected String	annotationLinkType()	Returns the type of annotation link for this object
DatasetData	asDatasetData()
String	getDescription()	Gets the DatasetData description
List<ImageWrapper>	getImages(Client client)	Gets all images in the dataset available from OMERO.
List<ImageWrapper>	getImages(Client client, String name)	Gets all images in the dataset with a certain name from OMERO.
List<ImageWrapper>	getImagesKey(Client client, String key)	Gets all images in the dataset with a certain key
List<ImageWrapper>	getImagesLike(Client client, String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
List<ImageWrapper>	getImagesPairKeyValue(Client client, String key, String value)	Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesTagged(Client client, Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
String	getName()	Gets the DatasetData name
List<ProjectWrapper>	getProjects(Client client)	Retrieves the projects containing this dataset.
List<Long>	importAndReplaceImages(Client client, String path)	Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.
List<Long>	importAndReplaceImages(Client client, String path, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.
List<Long>	importImage(Client client, String path)	Imports one image file to the dataset in OMERO.
boolean	importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
void	refresh(Client client)	Refreshes the wrapped dataset.
void	removeImage(Client client, ImageWrapper image)	Removes an image from the dataset in OMERO.
List<ImageWrapper>	replaceImages(Client client, Collection<? extends ImageWrapper> oldImages, ImageWrapper newImage)	Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations and ROIs, and concatenating the descriptions (on new lines).
void	setDescription(String description)	Sets the description of the dataset.
void	setName(String name)	Sets the name of the dataset.

Methods inherited from class fr.igred.omero.repository.GenericRepositoryObjectWrapper

addAndReplaceFile, addAndReplaceFile, addFile, addFileAnnotation, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getTable, getTables, getTags, getValue, removeLink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, getCreated, getGroupId, getId, getOwner, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

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

Field Detail

ANNOTATION_LINK

public static final String ANNOTATION_LINK

See Also:

Constant Field Values

Constructor Detail

DatasetWrapper

public DatasetWrapper(String name,
                      String description)

Constructor of the DatasetWrapper class

Parameters:

name - Name of the dataset.

description - Description of the dataset.

DatasetWrapper

public DatasetWrapper(DatasetData dataset)

Constructor of the DatasetWrapper class

Parameters:

dataset - Dataset to be contained.

Method Detail

getName

public String getName()

Gets the DatasetData name

Specified by:

getName in class GenericRepositoryObjectWrapper<DatasetData>

Returns:

DatasetData name.

setName

public void setName(String name)

Sets the name of the dataset.

Parameters:

name - The name of the dataset. Mustn't be null.

Throws:

IllegalArgumentException - If the name is null.

asDatasetData

public DatasetData asDatasetData()

Returns:

the DatasetData contained.

getDescription

public String getDescription()

Gets the DatasetData description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<DatasetData>

Returns:

DatasetData description.

setDescription

public void setDescription(String description)

Sets the description of the dataset.

Parameters:

description - The description of the dataset.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object

Specified by:

annotationLinkType in class GenericRepositoryObjectWrapper<DatasetData>

Returns:

See above.

getProjects

public List<ProjectWrapper> getProjects(Client client)
                                 throws OMEROServerError,
                                        ServiceException,
                                        AccessException,
                                        ExecutionException

Retrieves the projects containing this dataset.

Parameters:

client - The client handling the connection.

Returns:

See above.

Throws:

OMEROServerError - Server error.

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImages

public List<ImageWrapper> getImages(Client client)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images in the dataset available from OMERO.

Parameters:

client - The client handling the connection.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImages

public List<ImageWrapper> getImages(Client client,
                                    String name)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all images in the dataset with a certain name from OMERO.

Parameters:

client - The client handling the connection.

name - Name searched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesLike

public List<ImageWrapper> getImagesLike(Client client,
                                        String motif)
                                 throws ServiceException,
                                        AccessException,
                                        ExecutionException

Gets all images in the dataset with a certain motif in their name from OMERO.

Parameters:

client - The client handling the connection.

motif - Motif searched in an image name.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

public List<ImageWrapper> getImagesTagged(Client client,
                                          TagAnnotationWrapper tag)
                                   throws ServiceException,
                                          AccessException,
                                          OMEROServerError,
                                          ExecutionException

Gets all images in the dataset tagged with a specified tag from OMERO.

Parameters:

client - The client handling the connection.

tag - TagAnnotationWrapper containing the tag researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesTagged

public List<ImageWrapper> getImagesTagged(Client client,
                                          Long tagId)
                                   throws ServiceException,
                                          AccessException,
                                          OMEROServerError,
                                          ExecutionException

Gets all images in the dataset tagged with a specified tag from OMERO.

Parameters:

client - The client handling the connection.

tagId - Id of the tag researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesKey

public List<ImageWrapper> getImagesKey(Client client,
                                       String key)
                                throws ServiceException,
                                       AccessException,
                                       ExecutionException

Gets all images in the dataset with a certain key

Parameters:

client - The client handling the connection.

key - Name of the key researched.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getImagesPairKeyValue

public List<ImageWrapper> getImagesPairKeyValue(Client client,
                                                String key,
                                                String value)
                                         throws ServiceException,
                                                AccessException,
                                                ExecutionException

Gets all images in the dataset with a certain key value pair from OMERO

Parameters:

client - The client handling the connection.

key - Name of the key researched.

value - Value associated with the key.

Returns:

ImageWrapper list.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addImages

public void addImages(Client client,
                      List<? extends ImageWrapper> images)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Adds a list of image to the dataset in OMERO.

Parameters:

client - The client handling the connection.

images - Image to add to the dataset.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addImage

public void addImage(Client client,
                     ImageWrapper image)
              throws ServiceException,
                     AccessException,
                     ExecutionException

Adds a single image to the dataset in OMERO

Parameters:

client - The client handling the connection.

image - Image to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

removeImage

public void removeImage(Client client,
                        ImageWrapper image)
                 throws ServiceException,
                        AccessException,
                        ExecutionException,
                        OMEROServerError,
                        InterruptedException

Removes an image from the dataset in OMERO.

Parameters:

client - The client handling the connection.

image - Image to remove.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

OMEROServerError - If the thread was interrupted.

InterruptedException - If block(long) does not return.

importImages

public boolean importImages(Client client,
                            String... paths)
                     throws ServiceException,
                            OMEROServerError,
                            AccessException,
                            IOException,
                            ExecutionException

Imports all images candidates in the paths to the dataset in OMERO.

Parameters:

client - The client handling the connection.

paths - Paths to the image files on the computer.

Returns:

If the import did not exit because of an error.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

IOException - Cannot read file.

ExecutionException - A Facility can't be retrieved or instantiated.

importImage

public List<Long> importImage(Client client,
                              String path)
                       throws ServiceException,
                              AccessException,
                              OMEROServerError,
                              ExecutionException

Imports one image file to the dataset in OMERO.

Parameters:

client - The client handling the connection.

path - Path to the image file on the computer.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

replaceImages

public List<ImageWrapper> replaceImages(Client client,
                                        Collection<? extends ImageWrapper> oldImages,
                                        ImageWrapper newImage)
                                 throws AccessException,
                                        ServiceException,
                                        ExecutionException,
                                        OMEROServerError,
                                        InterruptedException

Replaces (and unlinks) a collection of images from this dataset by a new image, after copying their annotations and ROIs, and concatenating the descriptions (on new lines).

Parameters:

client - The client handling the connection.

oldImages - The list of old images to replace.

newImage - The new image.

Returns:

The list of images that became orphaned once replaced.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

importAndReplaceImages

public List<Long> importAndReplaceImages(Client client,
                                         String path,
                                         GenericRepositoryObjectWrapper.ReplacePolicy policy)
                                  throws ServiceException,
                                         AccessException,
                                         OMEROServerError,
                                         ExecutionException,
                                         InterruptedException

Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking or even deleting them.

Parameters:

client - The client handling the connection.

path - Path to the image on the computer.

policy - Whether older images should be unlinked, deleted or deleted only if they become orphaned.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

importAndReplaceImages

public List<Long> importAndReplaceImages(Client client,
                                         String path)
                                  throws ServiceException,
                                         AccessException,
                                         OMEROServerError,
                                         ExecutionException,
                                         InterruptedException

Imports one image file to the dataset in OMERO and replace older images sharing the same name after copying their annotations and ROIs, and concatenating the descriptions (on new lines) by unlinking them.

Parameters:

client - The client handling the connection.

path - Path to the image on the computer.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - If block(long) does not return.

refresh

public void refresh(Client client)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Refreshes the wrapped dataset.

Parameters:

client - The client handling the connection.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.