ome.formats.importer

Class ImportLibrary

java.lang.Object

ome.formats.importer.ImportLibrary

All Implemented Interfaces:

IObservable

public class ImportLibrary
extends java.lang.Object
implements IObservable

support class for the proper usage of OMEROMetadataStoreClient and FormatReader instances. This library was factored out of ImportHandler to support ImportFixture

Since:

3.0-M3

Author:

Josh Moore, josh.moore at gmx.de

See Also:

FormatReader, OMEROMetadataStoreClient, ImportFixture, IObservable, IObserver

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	ImportLibrary.ImportCallback

Constructor Summary

Constructors

Constructor and Description
ImportLibrary(OMEROMetadataStoreClient client, OMEROWrapper reader) The default implementation of FileTransfer performs a no-op and therefore need not have FileTransfer.afterTransfer(int, List) as with the ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) constructor.
ImportLibrary(OMEROMetadataStoreClient client, OMEROWrapper reader, FileTransfer transfer) The library will not close the client instance.
ImportLibrary(OMEROMetadataStoreClient client, OMEROWrapper reader, FileTransfer transfer, int minutesToWait)
ImportLibrary(OMEROMetadataStoreClient client, OMEROWrapper reader, FileTransfer transfer, java.util.List<FileExclusion> exclusions, int minutesToWait)

Method Summary

Modifier and Type	Method and Description
boolean	addObserver(IObserver object) Add observer for notification
void	clear()
ImportLibrary.ImportCallback	createCallback(omero.grid.ImportProcessPrx proc, omero.cmd.HandlePrx handle, ImportContainer container)
omero.grid.ImportProcessPrx	createImport(ImportContainer container) Provide initial configuration to the server in order to create the ImportProcessPrx which will manage state server-side.
java.util.List<java.lang.String>	deleteFilesFromRepository(ImportContainer container) Delete files from the managed repository.
boolean	deleteObserver(IObserver object) Delete observer
boolean	importCandidates(ImportConfig config, ImportCandidates candidates) Primary user method for importing a number of import candidates.
java.util.List<omero.model.Pixels>	importImage(ImportContainer container, java.util.concurrent.ExecutorService threadPool, int index) Perform an image import uploading files if necessary.
java.util.List<omero.model.Pixels>	importImage(ImportContainer container, int index, int numDone, int total) Deprecated. now used by tests only
omero.model.OriginalFile	loadOriginalFile(omero.api.RawFileStorePrx uploader) Use RawFileStorePrx.getFileId() in order to load the OriginalFile that the service argument is acting on.
omero.grid.ManagedRepositoryPrx	lookupManagedRepository() Retrieves the first managed repository from the list of current active repositories.
void	notifyObservers(ImportEvent event) Notify observers of event
java.lang.String	uploadFile(omero.grid.ImportProcessPrx proc, java.lang.String[] srcFiles, int index, ChecksumProviderFactory cpf, TimeEstimator estimator, byte[] buf)
java.lang.String	uploadFile(omero.grid.ImportProcessPrx proc, java.lang.String[] srcFiles, int index, TimeEstimator estimator)
java.util.List<java.lang.String>	uploadFilesToRepository(java.lang.String[] srcFiles, omero.grid.ImportProcessPrx proc) Upload files to the managed repository.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ImportLibrary

public ImportLibrary(OMEROMetadataStoreClient client,
                     OMEROWrapper reader)

The default implementation of FileTransfer performs a no-op and therefore need not have FileTransfer.afterTransfer(int, List) as with the ImportLibrary(OMEROMetadataStoreClient, OMEROWrapper, FileTransfer) constructor.

Parameters:

client - client-side MetadataStore, not null

reader - a Bio-Formats reader (ignored), not null

ImportLibrary

public ImportLibrary(OMEROMetadataStoreClient client,
                     OMEROWrapper reader,
                     FileTransfer transfer)

The library will not close the client instance. The reader will be closed between calls to import. Note: the responsibility of closing FileTransfer.afterTransfer(int, List) falls to invokers of this method.

Parameters:

client - client-side MetadataStore, not null

reader - a Bio-Formats reader (ignored), not null

transfer - how files are to be transferred to the server

ImportLibrary

public ImportLibrary(OMEROMetadataStoreClient client,
                     OMEROWrapper reader,
                     FileTransfer transfer,
                     int minutesToWait)

ImportLibrary

public ImportLibrary(OMEROMetadataStoreClient client,
                     OMEROWrapper reader,
                     FileTransfer transfer,
                     java.util.List<FileExclusion> exclusions,
                     int minutesToWait)

Method Detail

addObserver

public boolean addObserver(IObserver object)

Description copied from interface: IObservable

Add observer for notification

Specified by:

addObserver in interface IObservable

Parameters:

object - - observer object

Returns:

true if added

deleteObserver

public boolean deleteObserver(IObserver object)

Description copied from interface: IObservable

Delete observer

Specified by:

deleteObserver in interface IObservable

Parameters:

object - - observer to delete

Returns:

true if deleted

notifyObservers

public void notifyObservers(ImportEvent event)

Description copied from interface: IObservable

Notify observers of event

Specified by:

notifyObservers in interface IObservable

Parameters:

event - - event that happened

importCandidates

public boolean importCandidates(ImportConfig config,
                                ImportCandidates candidates)

Primary user method for importing a number of import candidates.

Parameters:

config - The configuration information.

candidates - Hosts information about the files to import.

Returns:

if the import did not exit because of an error

deleteFilesFromRepository

public java.util.List<java.lang.String> deleteFilesFromRepository(ImportContainer container)
                                                           throws omero.ServerError

Delete files from the managed repository.

Parameters:

container - The current import container containing usedFiles to be deleted.

Returns:

List of files that could not be deleted.

Throws:

omero.ServerError - if file deletion failed

createImport

public omero.grid.ImportProcessPrx createImport(ImportContainer container)
                                         throws omero.ServerError,
                                                java.io.IOException

Provide initial configuration to the server in order to create the ImportProcessPrx which will manage state server-side.

Parameters:

container - the import container

Returns:

the new import process from the server

Throws:

omero.ServerError - if the import process could not be created

java.io.IOException - if the used files' absolute path could not be found

uploadFilesToRepository

public java.util.List<java.lang.String> uploadFilesToRepository(java.lang.String[] srcFiles,
                                                                omero.grid.ImportProcessPrx proc)

Upload files to the managed repository. This is done by first passing in the possibly absolute local file paths. A common selection of those are chosen and passed back to the client. As each file is written to the server, a message digest is kept updated of the bytes that are being written. These are then returned to the caller so they can be checked against the values found on the server.

Parameters:

srcFiles - the files to upload

proc - the server import process to use for the upload

Returns:

A list of the client-side (i.e. local) hashes for each file.

uploadFile

public java.lang.String uploadFile(omero.grid.ImportProcessPrx proc,
                                   java.lang.String[] srcFiles,
                                   int index,
                                   TimeEstimator estimator)
                            throws omero.ServerError,
                                   java.io.IOException

Throws:

omero.ServerError

java.io.IOException

uploadFile

public java.lang.String uploadFile(omero.grid.ImportProcessPrx proc,
                                   java.lang.String[] srcFiles,
                                   int index,
                                   ChecksumProviderFactory cpf,
                                   TimeEstimator estimator,
                                   byte[] buf)
                            throws omero.ServerError,
                                   java.io.IOException

Throws:

omero.ServerError

java.io.IOException

importImage

@Deprecated
public java.util.List<omero.model.Pixels> importImage(ImportContainer container,
                                                                  int index,
                                                                  int numDone,
                                                                  int total)
                                                           throws java.lang.Throwable

Deprecated. now used by tests only

Image import with only one file upload thread.

Throws:

java.lang.Throwable

See Also:

importImage(ImportContainer, ExecutorService, int)

importImage

public java.util.List<omero.model.Pixels> importImage(ImportContainer container,
                                                      java.util.concurrent.ExecutorService threadPool,
                                                      int index)
                                               throws FormatException,
                                                      java.io.IOException,
                                                      java.lang.Throwable

Perform an image import uploading files if necessary.

Parameters:

container - The import container which houses all the configuration values and target for the import.

threadPool - The pool of threads to use in file upload.

index - Index of the import in a set. 0 is safe if this is a singular import.

Returns:

List of Pixels that have been imported.

Throws:

FormatException - If there is a Bio-Formats image file format error during import.

java.io.IOException - If there is an I/O error.

omero.ServerError - If there is an error communicating with the OMERO server we're importing into.

java.lang.Throwable - If there is some other kind of error during import.

Since:

OMERO Beta 4.2.1.

createCallback

public ImportLibrary.ImportCallback createCallback(omero.grid.ImportProcessPrx proc,
                                                   omero.cmd.HandlePrx handle,
                                                   ImportContainer container)
                                            throws omero.ServerError

Throws:

omero.ServerError

lookupManagedRepository

public omero.grid.ManagedRepositoryPrx lookupManagedRepository()

Retrieves the first managed repository from the list of current active repositories.

Returns:

Active proxy for the legacy repository.

clear

public void clear()

loadOriginalFile

public omero.model.OriginalFile loadOriginalFile(omero.api.RawFileStorePrx uploader)
                                          throws omero.ServerError

Use RawFileStorePrx.getFileId() in order to load the OriginalFile that the service argument is acting on.

Parameters:

uploader - not null

Returns:

the original file

Throws:

omero.ServerError - if the file could not be identified and loaded