Package fr.igred.omero.repository

Class ProjectWrapper

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.AnnotatableWrapper<T>

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

fr.igred.omero.repository.ProjectWrapper

public class ProjectWrapper
extends GenericRepositoryObjectWrapper<ProjectData>

Class containing a ProjectData object.

Wraps function calls to the Project 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
ProjectWrapper(Client client, String name, String description)	Constructor of the ProjectWrapper class.
ProjectWrapper(ProjectData project)	Constructor of the ProjectWrapper class.

Method Summary

Modifier and Type	Method	Description
DatasetWrapper	addDataset(Client client, DatasetWrapper dataset)	Adds a dataset to the project in OMERO.
DatasetWrapper	addDataset(Client client, String name, String description)	Creates a dataset and adds it to the project in OMERO.
protected String	annotationLinkType()	Returns the type of annotation link for this object.
ProjectData	asProjectData()	Deprecated. Returns the ProjectData contained.
List<DatasetWrapper>	getDatasets()	Gets all the datasets in the project available from OMERO.
List<DatasetWrapper>	getDatasets(String name)	Gets the dataset with the specified name from OMERO
String	getDescription()	Gets the project description
List<ImageWrapper>	getImages(Client client)	Gets all images in the project available from OMERO.
List<ImageWrapper>	getImages(Client client, String name)	Gets all images in the project with a certain name from OMERO.
List<ImageWrapper>	getImages(Client client, String datasetName, String imageName)	Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
List<ImageWrapper>	getImagesKey(Client client, String key)	Deprecated. Gets all images in the project with a certain key
List<ImageWrapper>	getImagesLike(Client client, String motif)	Gets all images in the project with a certain motif in their name from OMERO.
List<ImageWrapper>	getImagesPairKeyValue(Client client, String key, String value)	Deprecated. Gets all images in the project with a certain key value pair from OMERO.
List<ImageWrapper>	getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesTagged(Client client, Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	getImagesWithKey(Client client, String key)	Gets all images in the project with a certain key
List<ImageWrapper>	getImagesWithKeyValuePair(Client client, String key, String value)	Gets all images in the project with a certain key value pair from OMERO.
String	getName()	Gets the ProjectData name
void	reload(Browser browser)	Reloads the project from OMERO.
void	removeDataset(Client client, DatasetWrapper dataset)	Removes a dataset from the project in OMERO.
void	setDescription(String description)	Sets the description of the project.
void	setName(String name)	Sets the name of the project.

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

ProjectWrapper

public ProjectWrapper(ProjectData project)

Constructor of the ProjectWrapper class.

Parameters:

project - ProjectData to be contained.

ProjectWrapper

public ProjectWrapper(Client client,
 String name,
 String description)
               throws ServiceException,
AccessException,
ExecutionException

Constructor of the ProjectWrapper class. Creates a new project and save it to OMERO.

Parameters:

client - The client handling the connection.

name - Project name.

description - Project description.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

Method Details

getName

public String getName()

Gets the ProjectData name

Specified by:

getName in class GenericRepositoryObjectWrapper<ProjectData>

Returns:

ProjectData name.

setName

public void setName(String name)

Sets the name of the project.

Parameters:

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

Throws:

IllegalArgumentException - If the name is null.

asProjectData

@Deprecated
public ProjectData asProjectData()

Deprecated.

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

Returns:

See above.

getDescription

public String getDescription()

Gets the project description

Specified by:

getDescription in class GenericRepositoryObjectWrapper<ProjectData>

Returns:

The project description.

setDescription

public void setDescription(String description)

Sets the description of the project.

Parameters:

description - The description of the project.

annotationLinkType

protected String annotationLinkType()

Returns the type of annotation link for this object.

Specified by:

annotationLinkType in class AnnotatableWrapper<ProjectData>

Returns:

See above.

getDatasets

public List<DatasetWrapper> getDatasets()

Gets all the datasets in the project available from OMERO.

Returns:

Collection of DatasetWrapper.

getDatasets

public List<DatasetWrapper> getDatasets(String name)

Gets the dataset with the specified name from OMERO

Parameters:

name - Name of the dataset searched.

Returns:

List of dataset with the given name.

addDataset

public DatasetWrapper addDataset(Client client,
 String name,
 String description)
                          throws ServiceException,
AccessException,
ExecutionException

Creates a dataset and adds it to the project in OMERO.

The project needs to be reloaded afterwards to list the new dataset.

Parameters:

client - The client handling the connection.

name - Dataset name.

description - Dataset description.

Returns:

The object saved in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

addDataset

public DatasetWrapper addDataset(Client client,
 DatasetWrapper dataset)
                          throws ServiceException,
AccessException,
ExecutionException

Adds a dataset to the project in OMERO.

Parameters:

client - The client handling the connection.

dataset - Dataset to be added.

Returns:

The object saved in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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

removeDataset

public void removeDataset(Client client,
 DatasetWrapper dataset)
                   throws ServiceException,
AccessException,
ExecutionException,
OMEROServerError,
InterruptedException

Removes a dataset from the project in OMERO.

Parameters:

client - The client handling the connection.

dataset - Dataset 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.

getImages

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

Gets all images in the project 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 project 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.

getImages

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

Gets all images with a certain name from datasets with the specified name inside this project on OMERO.

Parameters:

client - The client handling the connection.

datasetName - Expected dataset name.

imageName - Expected image name.

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 project 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 project tagged with a specified tag from OMERO.

Parameters:

client - The client handling the connection.

tag - TagAnnotationWrapper containing 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.

getImagesTagged

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

Gets all images in the project 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 project 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 project 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 project 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 project 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.

reload

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

Reloads the project from OMERO.

Overrides:

reload in class GenericRepositoryObjectWrapper<ProjectData>

Parameters:

browser - The client handling the connection.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

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