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

Packages that use ServiceException

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 ServiceException in fr.igred.omero

Methods in fr.igred.omero that throw ServiceException

Modifier and Type	Method	Description
void	GatewayWrapper.connect(java.lang.String hostname, int port, java.lang.String sessionId)	Connects to OMERO using a session ID.
void	GatewayWrapper.connect(java.lang.String hostname, int port, java.lang.String username, char[] password)	Connects the user to OMERO.
void	GatewayWrapper.connect(java.lang.String hostname, int port, java.lang.String username, char[] password, java.lang.Long groupID)	Connects the user to OMERO.
void	GatewayWrapper.connect(LoginCredentials cred)	Connects the user to OMERO.
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.
DatasetWrapper	Client.getDataset(java.lang.Long id)	Gets the dataset with the specified id from OMERO.
java.util.List<DatasetWrapper>	Client.getDatasets()	Gets all datasets available from OMERO.
java.util.List<DatasetWrapper>	Client.getDatasets(java.lang.Long... ids)	Gets the datasets with the specified ids from OMERO.
java.util.List<DatasetWrapper>	Client.getDatasets(java.lang.String name)	Gets all datasets with a certain name from OMERO.
GroupWrapper	Client.getGroup(java.lang.String groupName)	Returns the group which matches the name.
ImageWrapper	Client.getImage(java.lang.Long id)	Returns an ImageWrapper that contains the image with the specified id from OMERO.
java.util.List<ImageWrapper>	Client.getImages()	Gets all images owned by the current user.
java.util.List<ImageWrapper>	Client.getImages(java.lang.Long... ids)	Gets the images with the specified ids from OMERO
java.util.List<ImageWrapper>	Client.getImages(java.lang.String name)	Gets all images with a certain name from OMERO.
java.util.List<ImageWrapper>	Client.getImages(java.lang.String projectName, java.lang.String datasetName, java.lang.String imageName)	Gets all images with the name specified inside projects and datasets with the given names.
java.util.List<ImageWrapper>	Client.getImagesKey(java.lang.String key)	Gets all images with a certain key
java.util.List<ImageWrapper>	Client.getImagesLike(java.lang.String motif)	Gets all images with a certain motif in their name from OMERO.
java.util.List<ImageWrapper>	Client.getImagesPairKeyValue(java.lang.String key, java.lang.String value)	Gets all images with a certain key value pair 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.
OMEROMetadataStoreClient	GatewayWrapper.getImportStore()	Creates or recycles the import store.
PlateWrapper	Client.getPlate(java.lang.Long id)	Gets the plate with the specified id from OMERO.
java.util.List<PlateWrapper>	Client.getPlates()	Gets all plates available from OMERO.
java.util.List<PlateWrapper>	Client.getPlates(java.lang.Long... ids)	Gets the plates with the specified ids from OMERO.
ProjectWrapper	Client.getProject(java.lang.Long id)	Gets the project with the specified id from OMERO.
java.util.List<ProjectWrapper>	Client.getProjects()	Gets all projects available from OMERO.
java.util.List<ProjectWrapper>	Client.getProjects(java.lang.Long... ids)	Gets the projects with the specified ids from OMERO.
java.util.List<ProjectWrapper>	Client.getProjects(java.lang.String name)	Gets all projects with a certain name from OMERO.
ScreenWrapper	Client.getScreen(java.lang.Long id)	Gets the screen with the specified id from OMERO.
java.util.List<ScreenWrapper>	Client.getScreens()	Gets all screens available from OMERO.
java.util.List<ScreenWrapper>	Client.getScreens(java.lang.Long... ids)	Gets the screens with the specified ids from OMERO.
java.lang.String	GatewayWrapper.getSessionId()	Get the ID of the current session
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
ExperimenterWrapper	Client.getUser(java.lang.String username)	Returns the user which matches the username.
WellWrapper	Client.getWell(java.lang.Long id)	Gets the well with the specified id from OMERO.
java.util.List<WellWrapper>	Client.getWells()	Gets all wells available from OMERO.
java.util.List<WellWrapper>	Client.getWells(java.lang.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(java.lang.String username)	Gets the client associated with the username in the parameters.

Uses of ServiceException in fr.igred.omero.annotations

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

Modifier and Type	Method	Description
void	TableWrapper.addRows(Client client, ResultsTable results, java.lang.Long imageId, java.util.List<? extends Roi> ijRois)	Adds rows from an ImageJ ResultsTable.
void	TableWrapper.addRows(Client client, ResultsTable results, java.lang.Long imageId, java.util.List<? extends Roi> ijRois, java.lang.String roiProperty)	Adds rows from an ImageJ ResultsTable.
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.

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

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

Uses of ServiceException in fr.igred.omero.exception

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

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.handleServiceOrAccess(java.lang.Throwable t, java.lang.String message)	Helper method to convert an exception from: DSOutOfServiceException to ServiceException DSAccessException to AccessException
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 ServiceException in fr.igred.omero.repository

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

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.
DatasetWrapper	ProjectWrapper.addDataset(Client client, DatasetWrapper dataset)	Adds a dataset to the project in OMERO.
DatasetWrapper	ProjectWrapper.addDataset(Client client, java.lang.String name, java.lang.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, java.util.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, java.lang.String key, java.lang.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, java.lang.Long id)	Adds multiple tags to the object in OMERO, if possible.
void	GenericRepositoryObjectWrapper.addTag(Client client, java.lang.String name, java.lang.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, java.lang.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
java.util.List<java.io.File>	ImageWrapper.download(Client client, java.lang.String path)	Downloads the original files from the server.
java.awt.Color	ImageWrapper.getChannelColor(Client client, int index)	Gets the current color of the channel
java.awt.Color	ImageWrapper.getChannelImportedColor(Client client, int index)	Gets the original color of the channel
java.lang.String	ImageWrapper.getChannelName(Client client, int index)	Gets the name of the channel
java.util.List<ChannelWrapper>	ImageWrapper.getChannels(Client client)	Gets the image channels
java.util.List<DatasetWrapper>	ImageWrapper.getDatasets(Client client)	Retrieves the datasets containing this image
java.util.List<FileAnnotationWrapper>	GenericRepositoryObjectWrapper.getFileAnnotations(Client client)	Returns the file annotations
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<FolderWrapper>	ImageWrapper.getFolders(Client client)	Gets the list of Folder linked to the image Associate the folder to the image
java.util.List<ImageWrapper>	DatasetWrapper.getImages(Client client)	Gets all images in the dataset available from OMERO.
java.util.List<ImageWrapper>	DatasetWrapper.getImages(Client client, java.lang.String name)	Gets all images in the dataset with a certain name from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImages(Client client)	Gets all images in the project available from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImages(Client client, java.lang.String name)	Gets all images in the project with a certain name from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImages(Client client, java.lang.String datasetName, java.lang.String imageName)	Gets all images with a certain name from datasets with the specified name inside this project on OMERO.
java.util.List<ImageWrapper>	DatasetWrapper.getImagesKey(Client client, java.lang.String key)	Gets all images in the dataset with a certain key
java.util.List<ImageWrapper>	ProjectWrapper.getImagesKey(Client client, java.lang.String key)	Gets all images in the project with a certain key
java.util.List<ImageWrapper>	DatasetWrapper.getImagesLike(Client client, java.lang.String motif)	Gets all images in the dataset with a certain motif in their name from OMERO.
java.util.List<ImageWrapper>	ProjectWrapper.getImagesLike(Client client, java.lang.String motif)	Gets all images in the project with a certain motif in their name from OMERO.
java.util.List<ImageWrapper>	DatasetWrapper.getImagesPairKeyValue(Client client, java.lang.String key, java.lang.String value)	Gets all images in the dataset with a certain key value pair from OMERO
java.util.List<ImageWrapper>	ProjectWrapper.getImagesPairKeyValue(Client client, java.lang.String key, java.lang.String value)	Gets all images in the project with a certain key value pair from 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.Map<java.lang.String,java.lang.String>	GenericRepositoryObjectWrapper.getKeyValuePairs(Client client)	Gets the List of NamedValue (Key-Value pair) associated to an object.
java.util.List<MapAnnotationWrapper>	GenericRepositoryObjectWrapper.getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
java.util.List<PlateWrapper>	ImageWrapper.getPlates(Client client)	Retrieves the plates containing this image
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<ROIWrapper>	FolderWrapper.getROIs(Client client)	Gets the ROI contained in the folder associated with the image id set (an image need to be associated)
java.util.List<ROIWrapper>	ImageWrapper.getROIs(Client client)	Gets all ROIs linked to the image in OMERO
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.
TableWrapper	GenericRepositoryObjectWrapper.getTable(Client client, java.lang.Long fileId)	Gets a certain table linked to the object in OMERO.
java.util.List<TableWrapper>	GenericRepositoryObjectWrapper.getTables(Client client)	Gets all tables linked to the object in OMERO.
java.util.List<TagAnnotationWrapper>	GenericRepositoryObjectWrapper.getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
java.awt.image.BufferedImage	ImageWrapper.getThumbnail(Client client, int size)	Retrieves the image thumbnail of the specified size.
java.lang.String	GenericRepositoryObjectWrapper.getValue(Client client, java.lang.String key)	Gets the value from a Key-Value pair associated to the object.
WellWrapper	WellSampleWrapper.getWell(Client client)	Retrieves the well containing this well sample
java.util.List<WellWrapper>	ImageWrapper.getWells(Client client)	Retrieves the wells containing this image
java.util.List<WellWrapper>	PlateWrapper.getWells(Client client)	Gets all wells in the plate available from OMERO.
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	PixelsWrapper.loadPlanesInfo(Client client)	Loads the planes information.
void	DatasetWrapper.refresh(Client client)	Refreshes the wrapped dataset.
void	ProjectWrapper.refresh(Client client)	Refreshes the wrapped project.
void	ScreenWrapper.refresh(GatewayWrapper client)	Refreshes the wrapped screen.
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).
void	ImageWrapper.saveROI(Client client, ROIWrapper roi)	Links a ROI to the image in OMERO
java.util.List<ROIWrapper>	ImageWrapper.saveROIs(Client client, java.util.Collection<? extends ROIWrapper> rois)	Links ROIs 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[] xBounds, int[] yBounds, int[] cBounds, int[] zBounds, int[] tBounds)	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 ServiceException

Constructor	Description
FolderWrapper(Client client, java.lang.String name)	Constructor of the FolderWrapper class.
ProjectWrapper(Client client, java.lang.String name, java.lang.String description)	Constructor of the ProjectWrapper class.
ScreenWrapper(Client client, java.lang.String name, java.lang.String description)	Constructor of the ProjectWrapper class.

Uses of ServiceException in fr.igred.omero.roi

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

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