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

Packages that use OMEROServerError

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.
fr.igred.omero.roi	This package contains wrapper classes for OMERO shapes and ROIs.

Uses of OMEROServerError in fr.igred.omero

Methods in fr.igred.omero that throw OMEROServerError

Modifier and Type	Method	Description
long	AnnotatableWrapper.addAndReplaceFile(Client client, File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
long	AnnotatableWrapper.addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper table)	Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
void	AnnotatableWrapper.addAndReplaceTable(Client client, TableWrapper table, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	Client.delete(TableWrapper table)	Deprecated. 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.
void	GatewayWrapper.deleteFile(Long id)	Deletes a file from OMERO
void	GatewayWrapper.deleteFiles(Long... ids)	Deletes files from OMERO.
void	Client.deleteTable(TableWrapper table)	Deletes a table from OMERO.
void	Client.deleteTables(Collection<? extends TableWrapper> tables)	Deletes tables from OMERO.
List<IObject>	GatewayWrapper.findByQuery(String query)	Finds objects on OMERO through a database query.
List<DatasetWrapper>	Browser.getDatasets()	Gets all datasets available from OMERO.
List<DatasetWrapper>	Browser.getDatasets(ExperimenterWrapper experimenter)	Gets all datasets available from OMERO owned by a given user.
GroupWrapper	Client.getGroup(long groupId)	Returns the group which matches the group ID.
abstract List<ImageWrapper>	Browser.getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation from OMERO.
List<ImageWrapper>	Client.getImages(GenericAnnotationWrapper<?> annotation)	Gets all images with the specified annotation from OMERO.
List<ImageWrapper>	Browser.getImagesTagged(TagAnnotationWrapper tag)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	Browser.getImagesTagged(Long tagId)	Deprecated. Gets all images tagged with a specified tag from OMERO.
List<ImageWrapper>	Browser.getImagesWithKey(String key)	Gets all images with a certain key.
List<ImageWrapper>	Browser.getImagesWithKeyValuePair(String key, String value)	Gets all images with a certain key value pair from OMERO
List<MapAnnotationWrapper>	Browser.getMapAnnotations()	Gets the list of map annotations available to the user.
List<MapAnnotationWrapper>	Browser.getMapAnnotations(String key)	Gets the list of map annotations with the specified key available to the user.
List<MapAnnotationWrapper>	Browser.getMapAnnotations(String key, String value)	Gets the list of map annotations with the specified key and value available to the user.
List<DatasetWrapper>	Browser.getOrphanedDatasets()	Gets all orphaned datasets available from OMERO owned by the current user.
List<DatasetWrapper>	Browser.getOrphanedDatasets(ExperimenterWrapper experimenter)	Gets all orphaned datasets available from OMERO owned by a given user.
List<PlateWrapper>	Browser.getOrphanedPlates()	Gets all orphaned plates available from OMERO for the current user.
List<PlateWrapper>	Browser.getOrphanedPlates(ExperimenterWrapper experimenter)	Gets all orphaned plates available from OMERO owned by a given user.
TagAnnotationWrapper	Browser.getTag(Long id)	Gets a specific tag from the OMERO database.
List<TagAnnotationWrapper>	Browser.getTags()	Gets the list of tag annotations available to the user.
List<TagAnnotationWrapper>	Browser.getTags(String name)	Gets the list of tag annotations with the specified name available to the user.
ExperimenterWrapper	Client.getUser(long userId)	Returns the user which matches the user ID.
List<WellWrapper>	Browser.getWells()	Gets all wells available from OMERO.
List<WellWrapper>	Browser.getWells(ExperimenterWrapper experimenter)	Gets all wells available from OMERO owned by a given user.
void	AnnotatableWrapper.rate(Client client, int rating)	Rates the object (using a rating annotation).
protected void	AnnotatableWrapper.removeLink(Client client, String linkType, long childId)	Removes the link of the given type with the given child ID.
protected void	AnnotatableWrapper.removeLinks(Client client, String linkType, Collection<Long> childIds)	Removes the link of the given type with the given child IDs.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
<A extends GenericAnnotationWrapper<?>> void	AnnotatableWrapper.unlink(Client client, Collection<A> annotations)	Unlinks the given annotations from the current object.

Uses of OMEROServerError in fr.igred.omero.annotations

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

Modifier and Type	Method	Description
int	GenericAnnotationWrapper.countAnnotationLinks(Client client)	Returns the number of annotations links for this object.
List<DatasetWrapper>	GenericAnnotationWrapper.getDatasets(Client client)	Gets all datasets with this annotation from OMERO.
File	FileAnnotationWrapper.getFile(Client client, String path)	Returns the original file.
List<FolderWrapper>	GenericAnnotationWrapper.getFolders(Client client)	Gets all folders with this annotation from OMERO.
List<ImageWrapper>	GenericAnnotationWrapper.getImages(Client client)	Gets all images with this annotation from OMERO.
List<PlateAcquisitionWrapper>	GenericAnnotationWrapper.getPlateAcquisitions(Client client)	Gets all plate acquisitions with this annotation from OMERO.
List<PlateWrapper>	GenericAnnotationWrapper.getPlates(Client client)	Gets all plates with this annotation from OMERO.
List<ProjectWrapper>	GenericAnnotationWrapper.getProjects(Client client)	Gets all projects with this annotation from OMERO.
List<ScreenWrapper>	GenericAnnotationWrapper.getScreens(Client client)	Gets all screens with this annotation from OMERO.
List<TagAnnotationWrapper>	TagSetWrapper.getTags(Browser browser)	Reloads the tag set and returns the corresponding list of tags.
List<WellWrapper>	GenericAnnotationWrapper.getWells(Client client)	Gets all wells with this annotation from OMERO.
void	TagSetWrapper.reload(Browser browser)	Reloads the tag set from OMERO.

Uses of OMEROServerError in fr.igred.omero.exception

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

Modifier and Type	Method	Description
ExceptionHandler<T>	ExceptionHandler.handleException(String message)	Deprecated. Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught The appropriate exception if ServerError was caught (see ExceptionHandler.handleOMEROException(java.lang.Throwable, java.lang.String))
static void	ExceptionHandler.handleException(Throwable t, String message)	Deprecated. Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError
ExceptionHandler<T>	ExceptionHandler.handleServiceOrServer(String message)	Deprecated. Throws: ServiceException if DSOutOfServiceException was caught OMEROServerError if ServerError was caught
static void	ExceptionHandler.handleServiceOrServer(Throwable t, String message)	Deprecated. Helper method to convert an exception from: DSOutOfServiceException to ServiceException ServerError to OMEROServerError

Uses of OMEROServerError in fr.igred.omero.repository

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

Modifier and Type	Method	Description
List<File>	ImageWrapper.download(Client client, String path)	Downloads the original files from the server.
List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
List<ImageWrapper>	ImageWrapper.getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
FolderWrapper	ImageWrapper.getFolder(Client client, Long folderId)	Deprecated. Gets the folder with the specified id on OMERO.
List<FolderWrapper>	ImageWrapper.getFolders(Client client)	Gets the list of folders linked to this image.
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.
List<ProjectWrapper>	DatasetWrapper.getProjects(Client client)	Retrieves the projects containing this dataset.
List<ProjectWrapper>	ImageWrapper.getProjects(Client client)	Retrieves the projects containing this image
List<ScreenWrapper>	ImageWrapper.getScreens(Client client)	Retrieves the screens containing this image
List<ScreenWrapper>	PlateAcquisitionWrapper.getScreens(Client client)	Retrieves the screens containing the parent plates.
List<ScreenWrapper>	PlateWrapper.getScreens(Client client)	Retrieves the screens containing this plate.
List<ScreenWrapper>	WellSampleWrapper.getScreens(Client client)	Returns the screens containing the parent Well.
List<ScreenWrapper>	WellWrapper.getScreens(Client client)	Refreshes this well and retrieves the screens containing it.
BufferedImage	ImageWrapper.getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
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.
protected static List<Long>	GenericRepositoryObjectWrapper.importImage(GatewayWrapper client, DataObject target, String path)	Imports one image file to the target in OMERO.
List<Long>	ScreenWrapper.importImage(GatewayWrapper client, String path)	Imports one image file to the screen in OMERO.
boolean	DatasetWrapper.importImages(Client client, int threads, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
protected static boolean	GenericRepositoryObjectWrapper.importImages(GatewayWrapper client, DataObject target, int threads, String... paths)	Imports all images candidates in the paths to the target in OMERO.
boolean	ScreenWrapper.importImages(GatewayWrapper client, int threads, String... paths)	Imports all images candidates in the paths to the screen in OMERO.
boolean	ScreenWrapper.importImages(GatewayWrapper client, String... paths)	Imports all images candidates in the paths to the screen in OMERO.
boolean	ImageWrapper.isOrphaned(Client client)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).
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.
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).

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

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

Uses of OMEROServerError in fr.igred.omero.roi

Methods in fr.igred.omero.roi that throw OMEROServerError

Modifier and Type	Method	Description
void	ROIWrapper.saveROI(Client client)	Saves the ROI.