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
void	Client.delete(TableWrapper table)	Deletes a table from OMERO
void	Client.delete(GenericObjectWrapper<?> object)	Deletes an object from OMERO.
void	Client.delete(java.util.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(java.lang.Long id)	Deletes a file from OMERO
java.util.List<IObject>	GatewayWrapper.findByQuery(java.lang.String query)	Finds objects on OMERO through a database query.
java.util.List<DatasetWrapper>	Client.getDatasets()	Gets all datasets available from OMERO.
java.util.List<ImageWrapper>	Client.getImagesTagged(TagAnnotationWrapper tag)	Gets all images tagged with a specified tag from OMERO.
java.util.List<ImageWrapper>	Client.getImagesTagged(java.lang.Long tagId)	Gets all images tagged with a specified tag from OMERO.
TagAnnotationWrapper	Client.getTag(java.lang.Long id)	Gets a specific tag from the OMERO database
java.util.List<TagAnnotationWrapper>	Client.getTags()	Gets the list of TagAnnotationWrapper available to the user
java.util.List<TagAnnotationWrapper>	Client.getTags(java.lang.String name)	Gets the list of TagAnnotationWrapper with the specified name available to the user
java.util.List<WellWrapper>	Client.getWells()	Gets all wells available from OMERO.

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.
java.util.List<DatasetWrapper>	GenericAnnotationWrapper.getDatasets(Client client)	Gets all datasets with this tag from OMERO.
java.io.File	FileAnnotationWrapper.getFile(Client client, java.lang.String path)	Returns the original file.
java.util.List<ImageWrapper>	GenericAnnotationWrapper.getImages(Client client)	Gets all images with this tag from OMERO.
java.util.List<PlateWrapper>	GenericAnnotationWrapper.getPlates(Client client)	Gets all plates with this tag from OMERO.
java.util.List<ProjectWrapper>	GenericAnnotationWrapper.getProjects(Client client)	Gets all projects with this tag from OMERO.
java.util.List<ScreenWrapper>	GenericAnnotationWrapper.getScreens(Client client)	Gets all screens with this tag from OMERO.
java.util.List<WellWrapper>	GenericAnnotationWrapper.getWells(Client client)	Gets all wells with this tag from OMERO.

Uses of OMEROServerError in fr.igred.omero.exception

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

Modifier and Type	Method	Description
static void	ExceptionHandler.handleException(java.lang.Throwable t, java.lang.String message)	Helper method to convert an exception from: DSAccessException to AccessException DSOutOfServiceException to ServiceException ServerError to OMEROServerError
static void	ExceptionHandler.handleServiceOrServer(java.lang.Throwable t, java.lang.String message)	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
long	GenericRepositoryObjectWrapper.addAndReplaceFile(Client client, java.io.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	GenericRepositoryObjectWrapper.addAndReplaceFile(Client client, java.io.File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	GenericRepositoryObjectWrapper.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	GenericRepositoryObjectWrapper.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.
java.util.List<java.io.File>	ImageWrapper.download(Client client, java.lang.String path)	Downloads the original files from the server.
java.util.List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
java.util.List<ImageWrapper>	ImageWrapper.getFilesetImages(Client client)	Returns the list of images sharing the same fileset as the current image.
FolderWrapper	ImageWrapper.getFolder(Client client, java.lang.Long folderId)	Gets the folder with the specified id on OMERO.
java.util.List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
java.util.List<ImageWrapper>	DatasetWrapper.getImagesTagged(Client client, java.lang.Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, TagAnnotationWrapper tag)	Gets all images in the project tagged with a specified tag from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImagesTagged(Client client, java.lang.Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
java.util.List<ProjectWrapper>	DatasetWrapper.getProjects(Client client)	Retrieves the projects containing this dataset.
java.util.List<ProjectWrapper>	ImageWrapper.getProjects(Client client)	Retrieves the projects containing this image
java.util.List<ScreenWrapper>	ImageWrapper.getScreens(Client client)	Retrieves the screens containing this image
java.util.List<ScreenWrapper>	PlateWrapper.getScreens(Client client)	Retrieves the screens containing this dataset.
java.awt.image.BufferedImage	ImageWrapper.getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
java.util.List<java.lang.Long>	DatasetWrapper.importAndReplaceImages(Client client, java.lang.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.
java.util.List<java.lang.Long>	DatasetWrapper.importAndReplaceImages(Client client, java.lang.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.
java.util.List<java.lang.Long>	DatasetWrapper.importImage(Client client, java.lang.String path)	Imports one image file to the dataset in OMERO.
protected static java.util.List<java.lang.Long>	GenericRepositoryObjectWrapper.importImage(GatewayWrapper client, DataObject target, java.lang.String path)	Imports one image file to the target in OMERO.
java.util.List<java.lang.Long>	ScreenWrapper.importImage(GatewayWrapper client, java.lang.String path)	Imports one image file to the screen in OMERO.
boolean	DatasetWrapper.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
protected static boolean	GenericRepositoryObjectWrapper.importImages(GatewayWrapper client, DataObject target, java.lang.String... paths)	Imports all images candidates in the paths to the target in OMERO.
boolean	ScreenWrapper.importImages(GatewayWrapper client, java.lang.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.
protected void	GenericRepositoryObjectWrapper.removeLink(Client client, java.lang.String linkType, long childId)	Removes the link of the given type with the given child ID.
java.util.List<ImageWrapper>	DatasetWrapper.replaceImages(Client client, java.util.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).
<A extends GenericAnnotationWrapper<?>> void	GenericRepositoryObjectWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.

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

Constructor	Description
FolderWrapper(Client client, java.lang.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.