Package fr.igred.omero.repository

Class DatasetWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

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

fr.igred.omero.repository.DatasetWrapper

public class DatasetWrapper
extends GenericRepositoryObjectWrapper<DatasetData>

Class containing a DatasetData object.

Wraps function calls to 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 final String	ANNOTATION_LINK	Annotation link name for this type of object

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()	Deprecated. Returns the DatasetData contained.
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)	Deprecated. 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)	Deprecated. 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.
List<ImageWrapper>	getImagesWithKey(Client client, String key)	Gets all images in the dataset with a certain key
List<ImageWrapper>	getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the dataset with a certain key value pair 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, int threads, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
void	reload(Browser browser)	Reloads the dataset from OMERO.
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

copyAnnotationLinks, importImage, importImages, refresh

Methods inherited from class fr.igred.omero.AnnotatableWrapper

addAndReplaceFile, addAndReplaceFile, addAndReplaceTable, addAndReplaceTable, addFile, addFileAnnotation, addKeyValuePair, addMapAnnotation, addPairKeyValue, addTable, addTag, addTag, addTag, addTags, addTags, copyAnnotationLinks, getAnnotations, getFileAnnotations, getKeyValuePairs, getMapAnnotations, getMyRating, getRatings, getTable, getTables, getTags, getValue, isLinked, link, link, linkIfNotLinked, rate, removeLink, unlink

Methods inherited from class fr.igred.omero.GenericObjectWrapper

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

Methods inherited from class java.lang.Object

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

Field Details

ANNOTATION_LINK

public static final String ANNOTATION_LINK

Annotation link name for this type of object

See Also:

• Constant Field Values

Constructor Details

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 Details

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

@Deprecated
public DatasetData asDatasetData()

Deprecated.

Returns the DatasetData contained. Use GenericObjectWrapper.asDataObject() instead.

Returns:

See above.

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 AnnotatableWrapper<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:

See above.

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:

See above.

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:

See above.

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 - The tag annotation.

Returns:

See above.

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:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

OMEROServerError - Server error.

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

getImagesKey

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

Deprecated.

Gets all images in the dataset with a certain key

Parameters:

client - The client handling the connection.

key - Name of the key researched.

Returns:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesWithKey

public List<ImageWrapper> getImagesWithKey(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:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesPairKeyValue

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

Deprecated.

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:

See above.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

getImagesWithKeyValuePair

public List<ImageWrapper> getImagesWithKeyValuePair(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:

See above.

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 - Server error.

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.

importImages

public boolean importImages(Client client,
 int threads,
 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.

threads - The number of threads (same value used for filesets and uploads).

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.

reload

public void reload(Browser browser)
            throws ServiceException,
AccessException,
ExecutionException

Reloads the dataset from OMERO.

Overrides:

reload in class GenericRepositoryObjectWrapper<DatasetData>

Parameters:

browser - The data browser.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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