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

Packages that use ServerException

Package	Description
fr.igred.omero	This package contains the main interfaces and abstract classes to handle OME Remote Objects.
fr.igred.omero.annotations	This package contains interfaces and classes for handling annotations.
fr.igred.omero.client	This package contains the client interfaces used to interact with an OMERO server and a class implementing them.
fr.igred.omero.containers	This package contains interfaces and classes related to the hierarchical organization for images,
fr.igred.omero.core	This package contains interfaces and classes to handle images and their content, such as pixels, channels or planes.
fr.igred.omero.exception	This package contains wrapper classes for exceptions and an exception handler.
fr.igred.omero.screen	This package contains interfaces and classes related to the HCS organization, e.g.

Uses of ServerException in fr.igred.omero

Methods in fr.igred.omero that throw ServerException

Modifier and Type	Method	Description
default long	Annotatable.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	Annotatable.addAndReplaceFile(Client client, java.io.File file, ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
long	AnnotatableWrapper.addAndReplaceFile(Client client, java.io.File file, ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
default void	Annotatable.addAndReplaceTable(Client client, Table 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	Annotatable.addAndReplaceTable(Client client, Table table, ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
void	AnnotatableWrapper.addAndReplaceTable(Client client, Table table, ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
java.util.List<Dataset>	ContainerLinked.getDatasets(Browser browser)	Retrieves the datasets linked to this object, either directly, or through parents/children.
java.util.List<Image>	ImageLinked.getImages(Browser browser)	Retrieves the images linked to this object, either directly, or through parents/children.
java.util.List<PlateAcquisition>	HCSLinked.getPlateAcquisitions(Browser browser)	Returns the plate acquisitions linked to this object, either directly, or through parents/children.
java.util.List<Plate>	HCSLinked.getPlates(Browser browser)	Returns the plates linked to this object, either directly, or through parents/children.
java.util.List<Project>	ContainerLinked.getProjects(Browser browser)	Retrieves the projects linked to this object, either directly, or through parents/children.
java.util.List<Screen>	HCSLinked.getScreens(Browser browser)	Retrieves the screens linked to this object, either directly, or through parents/children.
java.util.List<Well>	HCSLinked.getWells(Browser browser)	Retrieves the wells linked to this object, either directly, or through parents/children.
protected static java.util.List<java.lang.Long>	RepositoryObjectWrapper.importImage(ConnectionHandler client, DataObject target, java.lang.String path)	Imports one image file to the target in OMERO.
protected static boolean	RepositoryObjectWrapper.importImages(ConnectionHandler client, DataObject target, java.lang.String... paths)	Imports all images candidates in the paths to the target in OMERO.
void	Annotatable.rate(Client client, int rating)	Rates the object (using a rating annotation).
void	AnnotatableWrapper.rate(Client client, int rating)	Rates the object (using a rating annotation).
protected void	AnnotatableWrapper.removeLink(Client client, java.lang.String linkType, long childId)	Removes the link of the given type with the given child ID.
<A extends Annotation> void	Annotatable.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.
<A extends Annotation> void	AnnotatableWrapper.unlink(Client client, A annotation)	Unlinks the given annotation from the current object.

Uses of ServerException in fr.igred.omero.annotations

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

Modifier and Type	Method	Description
default int	Annotation.countAnnotationLinks(Browser browser)	Returns the number of annotations links for this object.
java.util.List<Dataset>	AnnotationWrapper.getDatasets(Browser browser)	Gets all datasets with this annotation from OMERO.
java.io.File	FileAnnotation.getFile(ConnectionHandler client, java.lang.String path)	Returns the original file.
java.io.File	FileAnnotationWrapper.getFile(ConnectionHandler client, java.lang.String path)	Returns the original file.
java.util.List<Folder>	Annotation.getFolders(Browser browser)	Gets all folders with this annotation from OMERO.
java.util.List<Folder>	AnnotationWrapper.getFolders(Browser browser)	Gets all folders with this annotation from OMERO.
java.util.List<Image>	AnnotationWrapper.getImages(Browser browser)	Gets all images with this annotation from OMERO.
java.util.List<PlateAcquisition>	AnnotationWrapper.getPlateAcquisitions(Browser browser)	Gets all plate acquisitions with this annotation from OMERO.
java.util.List<Plate>	AnnotationWrapper.getPlates(Browser browser)	Gets all plates with this annotation from OMERO.
java.util.List<Project>	AnnotationWrapper.getProjects(Browser browser)	Gets all projects with this annotation from OMERO.
java.util.List<Screen>	AnnotationWrapper.getScreens(Browser browser)	Gets all screens with this annotation from OMERO.
java.util.List<Well>	AnnotationWrapper.getWells(Browser browser)	Gets all wells with this annotation from OMERO.

Uses of ServerException in fr.igred.omero.client

Methods in fr.igred.omero.client that throw ServerException

Modifier and Type	Method	Description
default void	DataManager.delete(Table table)	Deletes a table from OMERO.
default void	DataManager.delete(RemoteObject object)	Deletes an object from OMERO.
default void	DataManager.delete(java.util.Collection<? extends RemoteObject> objects)	Deletes multiple objects from OMERO.
default void	DataManager.delete(java.util.List<IObject> objects)	Deletes multiple objects from OMERO.
default void	DataManager.delete(IObject object)	Deletes an object from OMERO.
default void	DataManager.deleteFile(java.lang.Long id)	Deletes a file from OMERO
default java.util.List<IObject>	Browser.findByQuery(java.lang.String query)	Finds objects on OMERO through a database query.
default java.util.List<Dataset>	Browser.getDatasets()	Gets all datasets available from OMERO.
default java.util.List<Dataset>	Browser.getDatasets(Experimenter experimenter)	Gets all datasets available from OMERO owned by a given user.
default java.util.List<Image>	Browser.getImages(Annotation annotation)	Gets all images with the specified annotation from OMERO.
default java.util.List<Image>	Browser.getImagesWithKey(java.lang.String key)	Gets all images with a certain key.
default java.util.List<Image>	Browser.getImagesWithKeyValuePair(java.lang.String key, java.lang.String value)	Gets all images with a certain key value pair from OMERO
default java.util.List<MapAnnotation>	Browser.getMapAnnotations()	Gets the list of map annotations available to the user.
default java.util.List<MapAnnotation>	Browser.getMapAnnotations(java.lang.String key)	Gets the list of map annotations with the specified key available to the user.
default java.util.List<MapAnnotation>	Browser.getMapAnnotations(java.lang.String key, java.lang.String value)	Gets the list of map annotations with the specified key and value available to the user.
default java.util.List<TagAnnotation>	Browser.getTags()	Gets the list of tag annotations available to the user.
default java.util.List<TagAnnotation>	Browser.getTags(java.lang.String name)	Gets the list of tag annotations with the specified name available to the user.
default java.util.List<Well>	Browser.getWells()	Gets all wells available from OMERO.
default java.util.List<Well>	Browser.getWells(Experimenter experimenter)	Gets all wells available from OMERO owned by a given user.

Uses of ServerException in fr.igred.omero.containers

Methods in fr.igred.omero.containers that throw ServerException

Modifier and Type	Method	Description
default java.util.List<Image>	Dataset.getImagesTagged(Browser browser, TagAnnotation tag)	Gets all images in the dataset tagged with a specified tag from OMERO.
default java.util.List<Image>	Dataset.getImagesTagged(Browser browser, java.lang.Long tagId)	Gets all images in the dataset tagged with a specified tag from OMERO.
default java.util.List<Image>	Project.getImagesTagged(Browser browser, TagAnnotation tag)	Gets all images in the project tagged with a specified tag from OMERO.
default java.util.List<Image>	Project.getImagesTagged(Browser browser, java.lang.Long tagId)	Gets all images in the project tagged with a specified tag from OMERO.
default java.util.List<Project>	Dataset.getProjects(Browser browser)	Retrieves the projects containing this dataset.
default java.util.List<java.lang.Long>	Dataset.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.
default java.util.List<java.lang.Long>	Dataset.importAndReplaceImages(Client client, java.lang.String path, 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>	Dataset.importImage(Client client, java.lang.String path)	Imports one image file to the dataset in OMERO.
java.util.List<java.lang.Long>	DatasetWrapper.importImage(Client client, java.lang.String path)	Imports one image file to the dataset in OMERO.
boolean	Dataset.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
boolean	DatasetWrapper.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the dataset in OMERO.
void	Project.removeDataset(Client client, Dataset dataset)	Removes a dataset from the project in OMERO.
void	ProjectWrapper.removeDataset(Client client, Dataset dataset)	Removes a dataset from the project in OMERO.
void	Dataset.removeImage(Client client, Image image)	Removes an image from the dataset in OMERO.
void	DatasetWrapper.removeImage(Client client, Image image)	Removes an image from the dataset in OMERO.
default java.util.List<Image>	Dataset.replaceImages(Client client, java.util.Collection<? extends Image> oldImages, Image 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).

Uses of ServerException in fr.igred.omero.core

Methods in fr.igred.omero.core that throw ServerException

Modifier and Type	Method	Description
java.util.List<java.io.File>	Image.download(ConnectionHandler client, java.lang.String path)	Downloads the original files from the server.
java.util.List<java.io.File>	ImageWrapper.download(ConnectionHandler client, java.lang.String path)	Downloads the original files from the server.
default java.util.List<Dataset>	Image.getDatasets(Browser browser)	Retrieves the datasets containing this image
default java.util.List<Image>	Image.getFilesetImages(Browser browser)	Returns the list of images sharing the same fileset as the current image.
default java.util.List<Folder>	Image.getFolders(Browser browser)	Gets the list of folders linked to this image.
default java.util.List<Project>	Image.getProjects(Browser browser)	Retrieves the projects containing this image.
default java.util.List<Screen>	Image.getScreens(Browser browser)	Retrieves the screens containing this image
java.awt.image.BufferedImage	Image.getThumbnail(ConnectionHandler client, int size)	Retrieves the image thumbnail of the specified size.
java.awt.image.BufferedImage	ImageWrapper.getThumbnail(ConnectionHandler client, int size)	Retrieves the image thumbnail of the specified size.
default boolean	Image.isOrphaned(Browser browser)	Checks if image is orphaned (not in a WellSample nor linked to a dataset).

Uses of ServerException in fr.igred.omero.exception

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

Modifier and Type	Method	Description
ExceptionHandler<T>	ExceptionHandler.handleException(java.lang.String message)	Throws: AccessException if DSAccessException was caught ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught
ExceptionHandler<T>	ExceptionHandler.handleServiceOrServer(java.lang.String message)	Throws: ServiceException if DSOutOfServiceException was caught ServerException if ServerError was caught

Uses of ServerException in fr.igred.omero.screen

Methods in fr.igred.omero.screen that throw ServerException

Modifier and Type	Method	Description
default java.util.List<Screen>	Plate.getScreens(Browser browser)	Retrieves the screens containing this plate.
default java.util.List<Screen>	PlateAcquisition.getScreens(Browser browser)	Retrieves the screens containing the parent plates.
default java.util.List<Screen>	Well.getScreens(Browser browser)	Refreshes this well and retrieves the screens containing it.
default java.util.List<Screen>	WellSample.getScreens(Browser browser)	Returns the screens containing the parent Well.
java.util.List<java.lang.Long>	Screen.importImage(Client client, java.lang.String path)	Imports one image file to the screen in OMERO.
java.util.List<java.lang.Long>	ScreenWrapper.importImage(Client client, java.lang.String path)	Imports one image file to the screen in OMERO.
boolean	Screen.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the screen in OMERO.
boolean	ScreenWrapper.importImages(Client client, java.lang.String... paths)	Imports all images candidates in the paths to the screen in OMERO.