omero.grid

Class _ManagedRepositoryDisp

java.lang.Object

Ice.ObjectImpl

omero.grid._ManagedRepositoryDisp

All Implemented Interfaces:

Ice.Object, java.io.Serializable, java.lang.Cloneable, _ManagedRepositoryOperations, _ManagedRepositoryOperationsNC, _RepositoryOperations, _RepositoryOperationsNC, ManagedRepository, Repository

Direct Known Subclasses:

_ManagedRepositoryTie

public abstract class _ManagedRepositoryDisp
extends Ice.ObjectImpl
implements ManagedRepository

FS-enabled repository which can convert uploaded files into Images by using Bio-Formats to import them.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	__ids
static long	serialVersionUID

Fields inherited from interface omero.grid.ManagedRepository

ice_staticId

Constructor Summary

Constructors

Constructor and Description
_ManagedRepositoryDisp()

Method Summary

Modifier and Type	Method and Description
static Ice.DispatchStatus	___importFileset(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___importPaths(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___listChecksumAlgorithms(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___listImports(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___setChecksumAlgorithm(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___suggestChecksumAlgorithm(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
static Ice.DispatchStatus	___verifyChecksums(ManagedRepository __obj, IceInternal.Incoming __inS, Ice.Current __current)
Ice.DispatchStatus	__dispatch(IceInternal.Incoming in, Ice.Current __current)
protected void	__readImpl(IceInternal.BasicStream __is)
protected void	__writeImpl(IceInternal.BasicStream __os)
HandlePrx	deletePaths(java.lang.String[] paths, boolean recursively, boolean force) Delete several individual paths.
RawFileStorePrx	file(java.lang.String path, java.lang.String mode) Returns a special RawFileStore which permits only the operations set out in the options string ""wb"", ""a+"", etc.
RawFileStorePrx	fileById(long id)
boolean	fileExists(java.lang.String path) Returns true if the file or path exists within the repository.
protected void	ice_copyStateFrom(Ice.Object __obj)
java.lang.String	ice_id()
java.lang.String	ice_id(Ice.Current __current)
java.lang.String[]	ice_ids()
java.lang.String[]	ice_ids(Ice.Current __current)
boolean	ice_isA(java.lang.String s)
boolean	ice_isA(java.lang.String s, Ice.Current __current)
static java.lang.String	ice_staticId()
ImportProcessPrx	importFileset(Fileset fs, ImportSettings settings) Returns an ImportProcess which can be used to upload files.
ImportProcessPrx	importPaths(java.util.List<java.lang.String> filePaths) For clients without access to Bio-Formats, the simplified importPaths method allows passing solely the absolute path of the files to be uploaded (no directories) and all configuration happens server-side.
java.util.List<java.lang.String>	list(java.lang.String path) Returns a set of strings naming the files and directories in the directory denoted by an abstract pathname.
java.util.List<ChecksumAlgorithm>	listChecksumAlgorithms() Return the list of checksum algorithms supported by this repository for verifying the integrity of uploaded files.
java.util.List<OriginalFile>	listFiles(java.lang.String path) Returns an array of abstract pathname objects denoting the files in the directory denoted by an abstract pathname.
java.util.List<ImportProcessPrx>	listImports() List imports that are currently running in this importer.
void	makeDir(java.lang.String path, boolean parents) Create a directory at the given path.
java.lang.String	mimetype(java.lang.String path) Returns the best-guess mimetype for the given path.
OriginalFile	register(java.lang.String path, RString mimetype) Create an OriginalFile in the database for the given path.
OriginalFile	root() Return the OriginalFile descriptor for this Repository.
java.util.List<java.lang.Long>	setChecksumAlgorithm(ChecksumAlgorithm hasher, java.util.List<java.lang.Long> ids) Set the checksum algorithm for the original files identified by the given IDs and calculate their checksum accordingly.
ChecksumAlgorithm	suggestChecksumAlgorithm(java.util.List<ChecksumAlgorithm> supported) Suggest a checksum algorithm to use for ImportSettings.checksumAlgorithm according to the preferences set by the server administrator.
RMap	treeList(java.lang.String path) Similar to list but recursive and returns only primitive values for the file at each location.
java.util.List<java.lang.Long>	verifyChecksums(java.util.List<java.lang.Long> ids) Verify the checksum for the original files identified by the given IDs.

Methods inherited from class Ice.ObjectImpl

___ice_id, ___ice_ids, ___ice_isA, ___ice_ping, __checkMode, __read, __read, __readImpl, __write, __write, __writeImpl, clone, ice_dispatch, ice_dispatch, ice_operationAttributes, ice_ping, ice_ping, ice_postUnmarshal, ice_preMarshal

Methods inherited from class java.lang.Object

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

Methods inherited from interface omero.grid._ManagedRepositoryOperations

importFileset, importPaths, listChecksumAlgorithms, listImports, setChecksumAlgorithm, suggestChecksumAlgorithm, verifyChecksums

Methods inherited from interface Ice.Object

__read, __read, __write, __write, clone, ice_dispatch, ice_dispatch, ice_operationAttributes, ice_ping, ice_ping, ice_postUnmarshal, ice_preMarshal

Methods inherited from interface omero.grid._RepositoryOperations

deletePaths, file, fileById, fileExists, list, listFiles, makeDir, mimetype, register, root, treeList

Field Detail

__ids

public static final java.lang.String[] __ids

serialVersionUID

public static final long serialVersionUID

See Also:

Constant Field Values

Constructor Detail

_ManagedRepositoryDisp

public _ManagedRepositoryDisp()

Method Detail

ice_copyStateFrom

protected void ice_copyStateFrom(Ice.Object __obj)
                          throws java.lang.CloneNotSupportedException

Throws:

java.lang.CloneNotSupportedException

ice_isA

public boolean ice_isA(java.lang.String s)

Specified by:

ice_isA in interface Ice.Object

Overrides:

ice_isA in class Ice.ObjectImpl

ice_isA

public boolean ice_isA(java.lang.String s,
                       Ice.Current __current)

Specified by:

ice_isA in interface Ice.Object

Overrides:

ice_isA in class Ice.ObjectImpl

ice_ids

public java.lang.String[] ice_ids()

Specified by:

ice_ids in interface Ice.Object

Overrides:

ice_ids in class Ice.ObjectImpl

ice_ids

public java.lang.String[] ice_ids(Ice.Current __current)

Specified by:

ice_ids in interface Ice.Object

Overrides:

ice_ids in class Ice.ObjectImpl

ice_id

public java.lang.String ice_id()

Specified by:

ice_id in interface Ice.Object

Overrides:

ice_id in class Ice.ObjectImpl

ice_id

public java.lang.String ice_id(Ice.Current __current)

Specified by:

ice_id in interface Ice.Object

Overrides:

ice_id in class Ice.ObjectImpl

ice_staticId

public static java.lang.String ice_staticId()

importFileset

public final ImportProcessPrx importFileset(Fileset fs,
                                            ImportSettings settings)
                                     throws ServerError

Returns an ImportProcess which can be used to upload files. On _ImportProcessOperations.verifyUpload(java.util.List<java.lang.String>, Ice.Current), an Handle will be returned which can be watched for knowing when the server-side import is complete. Client paths set in the fileset entries must /-separate their components. Once the upload is complete, the ImportProcess must be closed. Once _HandleOperations.getResponse(Ice.Current) returns a non-null value, the handle instance can and must be closed.

Specified by:

importFileset in interface _ManagedRepositoryOperationsNC

Throws:

ServerError

importPaths

public final ImportProcessPrx importPaths(java.util.List<java.lang.String> filePaths)
                                   throws ServerError

For clients without access to Bio-Formats, the simplified importPaths method allows passing solely the absolute path of the files to be uploaded (no directories) and all configuration happens server-side. Much of the functionality provided via Fileset and ImportSettings is of course lost.

Specified by:

importPaths in interface _ManagedRepositoryOperationsNC

Throws:

ServerError

listChecksumAlgorithms

public final java.util.List<ChecksumAlgorithm> listChecksumAlgorithms()

Return the list of checksum algorithms supported by this repository for verifying the integrity of uploaded files. They are named as ""algorithm-integer"", integer being the bit width of the resulting hash code. It is possible for the same algorithm to be offered with different bit widths. They are listed in descending order of preference, as set by the server administrator, and any of them may be specified for ImportSettings.checksumAlgorithm.

Specified by:

listChecksumAlgorithms in interface _ManagedRepositoryOperationsNC

listImports

public final java.util.List<ImportProcessPrx> listImports()
                                                   throws ServerError

List imports that are currently running in this importer. These will be limited based on user/group membership for the Fileset object which is being created by the import. If the user has write permissions for the fileset, then the import will be included.

Specified by:

listImports in interface _ManagedRepositoryOperationsNC

Throws:

ServerError

setChecksumAlgorithm

public final java.util.List<java.lang.Long> setChecksumAlgorithm(ChecksumAlgorithm hasher,
                                                                 java.util.List<java.lang.Long> ids)
                                                          throws ServerError

Set the checksum algorithm for the original files identified by the given IDs and calculate their checksum accordingly. The files must be in this repository. Existing checksums are checked before being changed. If a checksum does not match, ServerError will be thrown; in this case some other files may already have had their checksum algorithm set. Returns the IDs of the original files that did not already have a checksum set for the given algorithm.

Specified by:

setChecksumAlgorithm in interface _ManagedRepositoryOperationsNC

Throws:

ServerError

suggestChecksumAlgorithm

public final ChecksumAlgorithm suggestChecksumAlgorithm(java.util.List<ChecksumAlgorithm> supported)

Suggest a checksum algorithm to use for ImportSettings.checksumAlgorithm according to the preferences set by the server administrator. Provide a list of the algorithms supported by the client, and the server will report which of them is most preferred by the server, or return null if none of them are supported.

Specified by:

suggestChecksumAlgorithm in interface _ManagedRepositoryOperationsNC

verifyChecksums

public final java.util.List<java.lang.Long> verifyChecksums(java.util.List<java.lang.Long> ids)
                                                     throws ServerError

Verify the checksum for the original files identified by the given IDs. The files must be in this repository. Returns the IDs of the original files whose checksums do not match the file on disk.

Specified by:

verifyChecksums in interface _ManagedRepositoryOperationsNC

Throws:

ServerError

deletePaths

public final HandlePrx deletePaths(java.lang.String[] paths,
                                   boolean recursively,
                                   boolean force)
                            throws ServerError

Delete several individual paths. Internally, this converts all of the paths into a single Delete2 command and submits it. If a ""recursively"" is true, then directories will be searched and all of their contained files will be placed before them in the delete order. When the directory is removed from the database, it will removed from the filesystem if and only if it is empty. If ""recursively"" is false, then the delete will produce an error according to the ""force"" flag. If ""force"" is false, this method attempts the delete of all given paths in a single transaction, and any failure will cause the entire transaction to fail. If ""force"" is true, however, then all the other deletes will succeed. which could possibly leave dangling files within no longer extant directories.

Specified by:

deletePaths in interface _RepositoryOperationsNC

Throws:

ServerError

file

public final RawFileStorePrx file(java.lang.String path,
                                  java.lang.String mode)
                           throws ServerError

Returns a special RawFileStore which permits only the operations set out in the options string ""wb"", ""a+"", etc. FIXME: Initially only ""r"" and ""rw"" are supported as these are handled directly by RandomAccessFile and so don't break the current implementation. Any call to that tries to break the options will throw an ApiUsageException. If a file exists at the given path, a ValidationException will be thrown.

Specified by:

file in interface _RepositoryOperationsNC

Throws:

ServerError

fileById

public final RawFileStorePrx fileById(long id)
                               throws ServerError

Specified by:

fileById in interface _RepositoryOperationsNC

Throws:

ServerError

fileExists

public final boolean fileExists(java.lang.String path)
                         throws ServerError

Returns true if the file or path exists within the repository. In other words, if a call on `dirname path` to listFiles would return an object for this path.

Specified by:

fileExists in interface _RepositoryOperationsNC

Throws:

ServerError

list

public final java.util.List<java.lang.String> list(java.lang.String path)
                                            throws ServerError

Returns a set of strings naming the files and directories in the directory denoted by an abstract pathname.

Specified by:

list in interface _RepositoryOperationsNC

Throws:

ServerError

listFiles

public final java.util.List<OriginalFile> listFiles(java.lang.String path)
                                             throws ServerError

Returns an array of abstract pathname objects denoting the files in the directory denoted by an abstract pathname. It is expected that at a minimum the ""name"", ""path"", ""size"" and ""mtime"" attributes will be present for each OriginalFile instance.

Specified by:

listFiles in interface _RepositoryOperationsNC

Throws:

ServerError

makeDir

public final void makeDir(java.lang.String path,
                          boolean parents)
                   throws ServerError

Create a directory at the given path. If parents is true, then all preceding paths will be generated and no exception will be thrown if the directory already exists. Otherwise, all parent directories must exist in both the DB and on the filesystem and be readable.

Specified by:

makeDir in interface _RepositoryOperationsNC

Throws:

ServerError

mimetype

public final java.lang.String mimetype(java.lang.String path)
                                throws ServerError

Returns the best-guess mimetype for the given path.

Specified by:

mimetype in interface _RepositoryOperationsNC

Throws:

ServerError

register

public final OriginalFile register(java.lang.String path,
                                   RString mimetype)
                            throws ServerError

Create an OriginalFile in the database for the given path.

Specified by:

register in interface _RepositoryOperationsNC

Throws:

ServerError

root

public final OriginalFile root()
                        throws ServerError

Return the OriginalFile descriptor for this Repository. It will have the path of the repository's root on the underlying filesystem.

Specified by:

root in interface _RepositoryOperationsNC

Throws:

ServerError

treeList

public final RMap treeList(java.lang.String path)
                    throws ServerError

Similar to list but recursive and returns only primitive values for the file at each location. Guaranteed for each path is only the values id and mimetype. After a call to unwrap, the returned RMap for a call to treeList("/user_1/dir0") might look something like:

 
 {
 "/user_1/dir0/file1.txt" :
 {
 "id":10,
 "mimetype":
 "binary",
 "size": 10000L
 },

 "/user_1/dir0/dir1" :
 {
 "id": 100,
 "mimetype": "Directory",
 "size": 0L,
 "files":
 {
 "/user_1/dir0/dir1/file1indir.txt" :
 {
 "id": 1,
 "mimetype": "png",
 "size": 500
 }
 }
 }
 }
 
 

Specified by:

treeList in interface _RepositoryOperationsNC

Throws:

ServerError

___importFileset

public static Ice.DispatchStatus ___importFileset(ManagedRepository __obj,
                                                  IceInternal.Incoming __inS,
                                                  Ice.Current __current)

___importPaths

public static Ice.DispatchStatus ___importPaths(ManagedRepository __obj,
                                                IceInternal.Incoming __inS,
                                                Ice.Current __current)

___listImports

public static Ice.DispatchStatus ___listImports(ManagedRepository __obj,
                                                IceInternal.Incoming __inS,
                                                Ice.Current __current)

___listChecksumAlgorithms

public static Ice.DispatchStatus ___listChecksumAlgorithms(ManagedRepository __obj,
                                                           IceInternal.Incoming __inS,
                                                           Ice.Current __current)

___suggestChecksumAlgorithm

public static Ice.DispatchStatus ___suggestChecksumAlgorithm(ManagedRepository __obj,
                                                             IceInternal.Incoming __inS,
                                                             Ice.Current __current)

___verifyChecksums

public static Ice.DispatchStatus ___verifyChecksums(ManagedRepository __obj,
                                                    IceInternal.Incoming __inS,
                                                    Ice.Current __current)

___setChecksumAlgorithm

public static Ice.DispatchStatus ___setChecksumAlgorithm(ManagedRepository __obj,
                                                         IceInternal.Incoming __inS,
                                                         Ice.Current __current)

__dispatch

public Ice.DispatchStatus __dispatch(IceInternal.Incoming in,
                                     Ice.Current __current)

Specified by:

__dispatch in interface Ice.Object

Overrides:

__dispatch in class Ice.ObjectImpl

__writeImpl

protected void __writeImpl(IceInternal.BasicStream __os)

Overrides:

__writeImpl in class Ice.ObjectImpl

__readImpl

protected void __readImpl(IceInternal.BasicStream __is)

Overrides:

__readImpl in class Ice.ObjectImpl