Uses of Class
fr.igred.omero.exception.AccessException

Packages that use AccessException

Package	Description
fr.igred.omero	This package contains abstract wrapper classes for the OMERO Gateway and the basic OMERO object.
fr.igred.omero.annotations	This package contains wrapper classes for annotations.
fr.igred.omero.exception	This package contains wrapper classes for exceptions and an exception handler.
fr.igred.omero.repository	This package contains classes related to the hierarchical organization for images.

Uses of AccessException in fr.igred.omero

Methods in fr.igred.omero that throw AccessException

Modifier and Type	Method	Description
void	Client.delete(TableWrapper table)	Deletes a table from OMERO
void	Client.delete(GenericObjectWrapper<?> object)	Deletes an object from OMERO.
void	Client.delete(Collection<? extends GenericObjectWrapper<?>> objects)	Deletes multiple objects from OMERO.
protected static void	GenericObjectWrapper.delete(Client client, IObject object)	Deletes an object from OMERO.
void	GatewayWrapper.deleteFile(Long id)	Deletes a file from OMERO
DatasetWrapper	Client.getDataset(Long id)	Gets the dataset with the specified id from OMERO.
List<DatasetWrapper>	Client.getDatasets()	Gets all datasets available from OMERO.
List<DatasetWrapper>	Client.getDatasets(Long... ids)	Gets the datasets with the specified ids from OMERO.
List<DatasetWrapper>	Client.getDatasets(String name)	Gets all datasets with a certain name from OMERO.
GroupWrapper	Client.getGroup(String groupName)	Returns the group which matches the name.
ImageWrapper	Client.getImage(Long id)	Returns an ImageWrapper that contains the image with the specified id from OMERO.
List<ImageWrapper>	Client.getImages()	Gets all images owned by the current user.
List<ImageWrapper>	Client.getImages(Long... ids)	Gets the images with the specified ids from OMERO
List<ImageWrapper>	Client.getImages(String name)	Gets all images with a certain name from OMERO.
List<ImageWrapper>	Client.getImages(String projectName, String datasetName, String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
List<ImageWrapper>	Client.getImagesKey(String key)	Gets all images with a certain key
List<ImageWrapper>	Client.getImagesLike(String motif)	Gets all images with a certain motif in their name from OMERO.
List<ImageWrapper>	Client.getImagesPairKeyValue(String key, String value)	Gets all images with a certain key value pair from OMERO
List<ImageWrapper>	Client.getImagesTagged(TagAnnotationWrapper tag)	Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	Client.getImagesTagged(Long tagId)	Gets all images tagged with a specified tag from OMERO.
PlateWrapper	Client.getPlate(Long id)	Gets the plate with the specified id from OMERO.
List<PlateWrapper>	Client.getPlates()	Gets all plates available from OMERO.
List<PlateWrapper>	Client.getPlates(Long... ids)	Gets the plates with the specified ids from OMERO.
ProjectWrapper	Client.getProject(Long id)	Gets the project with the specified id from OMERO.
List<ProjectWrapper>	Client.getProjects()	Gets all projects available from OMERO.
List<ProjectWrapper>	Client.getProjects(Long... ids)	Gets the projects with the specified ids from OMERO.
List<ProjectWrapper>	Client.getProjects(String name)	Gets all projects with a certain name from OMERO.
ScreenWrapper	Client.getScreen(Long id)	Gets the screen with the specified id from OMERO.
List<ScreenWrapper>	Client.getScreens()	Gets all screens available from OMERO.
List<ScreenWrapper>	Client.getScreens(Long... ids)	Gets the screens with the specified ids from OMERO.
ExperimenterWrapper	Client.getUser(String username)	Returns the user which matches the username.
WellWrapper	Client.getWell(Long id)	Gets the well with the specified id from OMERO.
List<WellWrapper>	Client.getWells()	Gets all wells available from OMERO.
List<WellWrapper>	Client.getWells(Long... ids)	Gets the wells with the specified ids from OMERO.
IObject	GatewayWrapper.save(IObject object)	Saves an object on OMERO.
void	GenericObjectWrapper.saveAndUpdate(Client client)	Saves and updates object.
Client	Client.sudoGetUser(String username)	Gets the client associated with the username in the parameters.

Uses of AccessException in fr.igred.omero.annotations

Methods in fr.igred.omero.annotations that throw AccessException

Modifier and Type	Method	Description
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<Roi> ijRois)	Adds rows from an ImageJ ResultsTable.
void	TableWrapper.addRows(Client client, ResultsTable results, Long imageId, List<Roi> ijRois, String roiProperty)	Adds rows from an ImageJ ResultsTable.
List<DatasetWrapper>	GenericAnnotationWrapper.getDatasets(Client client)	Gets all datasets with this tag from OMERO.
List<ImageWrapper>	GenericAnnotationWrapper.getImages(Client client)	Gets all images with this tag from OMERO.
List<PlateWrapper>	GenericAnnotationWrapper.getPlates(Client client)	Gets all plates with this tag from OMERO.
List<ProjectWrapper>	GenericAnnotationWrapper.getProjects(Client client)	Gets all projects with this tag from OMERO.
List<ScreenWrapper>	GenericAnnotationWrapper.getScreens(Client client)	Gets all screens with this tag from OMERO.
List<WellWrapper>	GenericAnnotationWrapper.getWells(Client client)	Gets all wells with this tag from OMERO.

Constructors in fr.igred.omero.annotations that throw AccessException

Constructor	Description
TableWrapper(Client client, ResultsTable results, Long imageId, List<Roi> ijRois)	Constructor of the class TableWrapper.
TableWrapper(Client client, ResultsTable results, Long imageId, List<Roi> ijRois, String roiProperty)	Constructor of the class TableWrapper.
TagAnnotationWrapper(Client client, String name, String description)	Constructor of the TagAnnotationWrapper class.

Uses of AccessException in fr.igred.omero.exception

Methods in fr.igred.omero.exception that throw AccessException

Modifier and Type	Method	Description
static void	ExceptionHandler.handleException(Throwable t, String message)	Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError
static void	ExceptionHandler.handleServiceOrAccess(Throwable t, String message)	Helper method to convert an exception from: DSOutOfServiceException to ServiceException DSAccessException to AccessException

Uses of AccessException in fr.igred.omero.repository

Methods in fr.igred.omero.repository that throw AccessException

Modifier and Type	Method	Description
long	GenericRepositoryObjectWrapper.addAndReplaceFile(Client client, File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them.
long	GenericRepositoryObjectWrapper.addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them.
DatasetWrapper	ProjectWrapper.addDataset(Client client, DatasetWrapper dataset)	Adds a dataset to the project in OMERO.
DatasetWrapper	ProjectWrapper.addDataset(Client client, String name, String description)	Adds a dataset to the project in OMERO.
void	GenericRepositoryObjectWrapper.addFileAnnotation(Client client, FileAnnotationWrapper annotation)	Links a file annotation to the object
void	DatasetWrapper.addImage(Client client, ImageWrapper image)	Adds a single image to the dataset in OMERO
void	DatasetWrapper.addImages(Client client, List<? extends ImageWrapper> images)	Adds a list of image to the dataset in OMERO.
void	GenericRepositoryObjectWrapper.addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)	Adds a List of Key-Value pair to the object
void	GenericRepositoryObjectWrapper.addPairKeyValue(Client client, String key, String value)	Adds a single Key-Value pair to the object.
void	FolderWrapper.addROI(Client client, ROIWrapper roi)	Add an ROI to the folder and associate it to the image id set(an image need to be associated)
void	GenericRepositoryObjectWrapper.addTable(Client client, TableWrapper table)	Adds a table to the object in OMERO
protected void	FolderWrapper.addTag(Client client, TagAnnotationData tagData)	Private function.
void	GenericRepositoryObjectWrapper.addTag(Client client, TagAnnotationWrapper tag)	Adds a tag to the object in OMERO, if possible.
void	GenericRepositoryObjectWrapper.addTag(Client client, Long id)	Adds multiple tags to the object in OMERO, if possible.
void	GenericRepositoryObjectWrapper.addTag(Client client, String name, String description)	Adds a newly created tag to the object in OMERO, if possible.
protected void	GenericRepositoryObjectWrapper.addTag(Client client, TagAnnotationData tagData)	Protected function.
protected void	PlateAcquisitionWrapper.addTag(Client client, TagAnnotationData tagData)	Protected function.
void	GenericRepositoryObjectWrapper.addTags(Client client, TagAnnotationWrapper... tags)	Adds multiple tag to the object in OMERO, if possible.
void	GenericRepositoryObjectWrapper.addTags(Client client, Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
void	GenericRepositoryObjectWrapper.copyAnnotationLinks(Client client, GenericRepositoryObjectWrapper<?> object)	Copies annotation links from some other object to this one
List<File>	ImageWrapper.download(Client client, String path)	Downloads the original files from the server.
double[][][][][]	PixelsWrapper.getAllPixels(Client client)	Returns an array containing the value for each voxel
double[][][][][]	PixelsWrapper.getAllPixels(Client client, int[] xBound, int[] yBound, int[] cBound, int[] zBound, int[] tBound)	Returns an array containing the value for each voxel corresponding to the bounds
Color	ImageWrapper.getChannelColor(Client client, int index)	Gets the current color of the channel
Color	ImageWrapper.getChannelImportedColor(Client client, int index)	Gets the original color of the channel
String	ImageWrapper.getChannelName(Client client, int index)	Gets the name of the channel
List<ChannelWrapper>	ImageWrapper.getChannels(Client client)	Gets the image channels
List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
List<FileAnnotationWrapper>	GenericRepositoryObjectWrapper.getFileAnnotations(Client client)	Returns the file annotations
List<ImageWrapper>	ImageWrapper.getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
List<FolderWrapper>	ImageWrapper.getFolders(Client client)	Gets the list of Folder linked to the image Associate the folder to the image
List<ImageWrapper>	DatasetWrapper.getImages(Client client)	Gets all images in the dataset available from OMERO.
List<ImageWrapper>	DatasetWrapper.getImages(Client client, String name)	Gets all images in the dataset with a certain name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client)	Gets all images in the project available from OMERO.
List<ImageWrapper>	ProjectWrapper.getImages(Client client, String name)	Gets all images in the project with a certain name from OMERO.
List<ImageWrapper>	ProjectWrapper.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>	DatasetWrapper.getImagesKey(Client client, String key)	Gets all images in the dataset with a certain key
List<ImageWrapper>	ProjectWrapper.getImagesKey(Client client, String key)	Gets all images in the project with a certain key
List<ImageWrapper>	DatasetWrapper.getImagesLike(Client client, String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesLike(Client client, String motif)	Gets all images in the project with a certain motif in their name from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesPairKeyValue(Client client, String key, String value)	Gets all images in the dataset with a certain key value pair from OMERO
List<ImageWrapper>	ProjectWrapper.getImagesPairKeyValue(Client client, String key, String value)	Gets all images in the project with a certain key value pair from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the project tagged with a specified tag from OMERO.
List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
Map<String,String>	GenericRepositoryObjectWrapper.getKeyValuePairs(Client client)	Gets the List of NamedValue (Key-Value pair) associated to an object.
List<MapAnnotationWrapper>	GenericRepositoryObjectWrapper.getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
List<ProjectWrapper>	DatasetWrapper.getProjects(Client client)	Retrieves the projects containing this dataset.
List<ProjectWrapper>	ImageWrapper.getProjects(Client client)	Retrieves the projects containing this image
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int bpp)	Returns an array containing the raw values for each voxel for each planes
byte[][][][]	PixelsWrapper.getRawPixels(Client client, int[] xBound, int[] yBound, int[] cBound, int[] zBound, int[] tBound, int bpp)	Returns an array containing the raw values for each voxel for each plane corresponding to the bounds
List<ROIWrapper>	FolderWrapper.getROIs(Client client)	Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
List<ROIWrapper>	ImageWrapper.getROIs(Client client)	Gets all ROIs linked to the image in OMERO
TableWrapper	GenericRepositoryObjectWrapper.getTable(Client client, Long fileId)	Gets a certain table linked to the object in OMERO
List<TableWrapper>	GenericRepositoryObjectWrapper.getTables(Client client)	Gets all tables linked to the object in OMERO.
List<TagAnnotationWrapper>	GenericRepositoryObjectWrapper.getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
String	GenericRepositoryObjectWrapper.getValue(Client client, String key)	Gets the value from a Key-Value pair associated to the object
List<WellWrapper>	PlateWrapper.getWells(Client client)	Gets all wells in the plate available from OMERO.
List<Long>	DatasetWrapper.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>	DatasetWrapper.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>	DatasetWrapper.importImage(Client client, String path)	Imports one image file to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
void	DatasetWrapper.refresh(Client client)	Refreshes the wrapped dataset.
void	ProjectWrapper.refresh(Client client)	Refreshes the wrapped project.
void	ProjectWrapper.removeDataset(Client client, DatasetWrapper dataset)	Removes a dataset from the project in OMERO.
void	DatasetWrapper.removeImage(Client client, ImageWrapper image)	Removes an image from the dataset in OMERO.
protected void	GenericRepositoryObjectWrapper.removeLink(Client client, String linkType, long childId)	Removes the link of the given type with the given child ID.
List<ImageWrapper>	DatasetWrapper.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	ImageWrapper.saveROI(Client client, ROIWrapper roi)	Links a ROI to the image in OMERO
ImagePlus	ImageWrapper.toImagePlus(Client client)	Generates the ImagePlus from the ij library corresponding to the image from OMERO WARNING : you need to include the ij library to use this function
ImagePlus	ImageWrapper.toImagePlus(Client client, int[] xBound, int[] yBound, int[] cBound, int[] zBound, int[] tBound)	Gets the imagePlus generated from the image from OMERO corresponding to the bound
ImagePlus	ImageWrapper.toImagePlus(Client client, ROIWrapper roi)	Gets the imagePlus from the image generated from the ROI.
<A extends GenericAnnotationWrapper<?>> void	GenericRepositoryObjectWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
void	FolderWrapper.unlinkAllROI(Client client)	Unlink all ROI, associated to the image set, in the folder.
void	FolderWrapper.unlinkROI(Client client, ROIWrapper roi)	Unlink an ROI, associated to the image set, in the folder.

Constructors in fr.igred.omero.repository that throw AccessException

Constructor	Description
ProjectWrapper(Client client, String name, String description)	Constructor of the ProjectWrapper class.