Package ome.services.blitz.repo

Class ManagedRepositoryI

java.lang.Object

ome.services.blitz.repo.PublicRepositoryI

ome.services.blitz.repo.ManagedRepositoryI

All Implemented Interfaces:

_ManagedRepositoryOperations, _RepositoryOperations, org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class ManagedRepositoryI
extends PublicRepositoryI
implements _ManagedRepositoryOperations

Extension of the PublicRepository API which only manages files under ${omero.data.dir}/ManagedRepository.

Since:

5.0

Nested Class Summary

Nested classes/interfaces inherited from class ome.services.blitz.repo.PublicRepositoryI

PublicRepositoryI.AMD_submit

Field Summary

Fields

Modifier and Type	Field	Description
protected FsFile	templateRoot

Fields inherited from class ome.services.blitz.repo.PublicRepositoryI

checksumAlgorithms, checksumProviderFactory, context, DIRECTORY_MIMETYPE, filePathRestrictions, IMPORT_LOG_MIMETYPE, repositoryDao, serverPaths

Constructor Summary

Constructors

Constructor	Description
ManagedRepositoryI(java.lang.String template, RepositoryDao dao)	Creates a ProcessContainer internally that will not be managed by background threads.
ManagedRepositoryI(java.lang.String template, RepositoryDao dao, ProcessContainer processes, ome.security.SecuritySystem securitySystem, ome.util.checksum.ChecksumProviderFactory checksumProviderFactory, java.lang.String checksumAlgorithmSupported, java.lang.String pathRules, java.lang.String rootSessionUuid, ome.system.Roles roles, java.util.Set<java.lang.String> managedRepoUuids)

Method Summary

Modifier and Type	Method	Description
protected CheckedPath	checkPath(java.lang.String path, ChecksumAlgorithm checksumAlgorithm)
protected CheckedPath	checkPath(java.lang.String path, ChecksumAlgorithm checksumAlgorithm, Ice.Current curr)	Create a new CheckedPath object based on the given user input.
void	clearFileCreationListener()	Clear the file creation listener for this thread.
protected FsFile	commonRoot(java.util.List<FsFile> paths)	From a list of paths, calculate the common root path that all share.
protected ImportProcessPrx	createImportProcess(Fileset fs, ImportLocation location, ImportSettings settings, Ice.Current __current)	Creating the process will register itself in an appropriate container (i.e.
protected FsFile	createTemplatePath(java.lang.Object consistentData, Ice.Current __current)	Expand the template path and create its directories with the correct ownership.
FsFile	createTemplatePath(java.lang.Object consistentData, ome.system.EventContext ctx, ome.system.ServiceFactory sf, org.hibernate.Session session, ome.util.SqlAction sql)	Expand the template path and create its directories with the correct ownership.
protected ImportProcessPrx	createUploadProcess(Fileset fs, ImportLocation location, ImportSettings settings, Ice.Current __current, boolean uploadOnly)	Creating the process will register itself in an appropriate container (i.e.
protected FsFile	expandTemplateRootOwnedPath(EventContext ctx, ome.system.ServiceFactory sf)	Expand the root-owned segment of the template path.
protected java.lang.Class<? extends loci.formats.FormatReader>	getReaderClass(Fileset fs, Ice.Current __current)	Get the suggested BioFormats Reader for the given Fileset.
ImportProcessPrx	importFileset(Fileset fs, ImportSettings settings, Ice.Current __current)	Return a template based directory path.
ImportProcessPrx	importPaths(java.util.List<java.lang.String> paths, Ice.Current __current)	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.
void	initialize(FileMaker fileMaker, java.lang.Long id, java.lang.String repoUuid)	Called by the internal repository once initialization has taken place.
java.util.List<ChecksumAlgorithm>	listChecksumAlgorithms(Ice.Current __current)	Return the list of checksum algorithms supported by this repository for verifying the integrity of uploaded files.
java.util.List<ImportProcessPrx>	listImports(Ice.Current __current)	List imports that are currently running in this importer.
protected void	makeCheckedDirs(java.util.LinkedList<CheckedPath> paths, boolean parents, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext)	Checks for the top-level user directory restriction before calling PublicRepositoryI.makeCheckedDirs(LinkedList, boolean, Session, ServiceFactory, SqlAction, EventContext)
void	makeDir(java.lang.String path, boolean parents, org.hibernate.Session session, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext)
java.util.List<java.lang.Long>	setChecksumAlgorithm(ChecksumAlgorithm toHasherWrapped, java.util.List<java.lang.Long> ids, Ice.Current __current)	Set the checksum algorithm for the original files identified by the given IDs and calculate their checksum accordingly.
void	setFileCreationListener(java.util.function.Consumer<CheckedPath> fileCreationListener)	Set the file creation listener for this thread that is notified of new files being created.
ChecksumAlgorithm	suggestChecksumAlgorithm(java.util.List<ChecksumAlgorithm> supported, Ice.Current __current)	Suggest a checksum algorithm to use for ImportSettings.checksumAlgorithm according to the preferences set by the server administrator.
protected ImportLocation	suggestImportPaths(FsFile relPath, FsFile basePath, java.util.List<FsFile> paths, java.lang.Class<? extends loci.formats.FormatReader> reader, ChecksumAlgorithm checksumAlgorithm, Ice.Current __current)	Take a relative path that the user would like to see in his or her upload area, and provide an import location instance whose paths correspond to existing directories corresponding to the sanitized file paths.
Ice.Object	tie()	Wrap the current instance with an TieBase so that it can be turned into a proxy.
protected ome.services.blitz.repo.ManagedRepositoryI.Paths	trimPaths(FsFile basePath, java.util.List<FsFile> fullPaths, java.lang.Class<? extends loci.formats.FormatReader> readerClass)	Trim off the start of long client-side paths.
ImportProcessPrx	uploadFileset(Fileset fs, ImportSettings settings, Ice.Current __current)	Return a template based directory path.
java.util.List<java.lang.Long>	verifyChecksums(java.util.List<java.lang.Long> ids, Ice.Current __current)	Verify the checksum for the original files identified by the given IDs.

Methods inherited from class ome.services.blitz.repo.PublicRepositoryI

createRepoRFS, deletePaths, file, fileById, fileExists, findInDb, findOrCreateInDb, findOrCreateInDb, getFactory, getRepoUuid, list, listFiles, makeAdjustedCurrent, makeCheckedDirs, makeDir, makeDir, mimetype, persistLogFile, publishMessage, register, root, rootPath, setApplicationContext, stackTraceAsString, submitRequest, submitRequest, sudo, treeList

Methods inherited from class java.lang.Object

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

Methods inherited from interface omero.grid._RepositoryOperations

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

Field Detail

templateRoot

protected FsFile templateRoot

Constructor Detail

ManagedRepositoryI

public ManagedRepositoryI(java.lang.String template,
                          RepositoryDao dao)
                   throws java.lang.Exception

Creates a ProcessContainer internally that will not be managed by background threads. Used primarily during testing.

Parameters:

template -

dao -

Throws:

java.lang.Exception

ManagedRepositoryI

public ManagedRepositoryI(java.lang.String template,
                          RepositoryDao dao,
                          ProcessContainer processes,
                          ome.security.SecuritySystem securitySystem,
                          ome.util.checksum.ChecksumProviderFactory checksumProviderFactory,
                          java.lang.String checksumAlgorithmSupported,
                          java.lang.String pathRules,
                          java.lang.String rootSessionUuid,
                          ome.system.Roles roles,
                          java.util.Set<java.lang.String> managedRepoUuids)
                   throws ServerError

Throws:

ServerError

Method Detail

tie

public Ice.Object tie()

Description copied from class: PublicRepositoryI

Wrap the current instance with an TieBase so that it can be turned into a proxy. This is required due to the subclassing between public repo instances.

Overrides:

tie in class PublicRepositoryI

initialize

public void initialize(FileMaker fileMaker,
                       java.lang.Long id,
                       java.lang.String repoUuid)
                throws ValidationException

Description copied from class: PublicRepositoryI

Called by the internal repository once initialization has taken place.

Overrides:

initialize in class PublicRepositoryI

Throws:

ValidationException

setFileCreationListener

public void setFileCreationListener(java.util.function.Consumer<CheckedPath> fileCreationListener)

Set the file creation listener for this thread that is notified of new files being created. Maintains only a weak reference to the given listener. Applies only for uses of makeCheckedDirs(LinkedList, boolean, Session, ServiceFactory, SqlAction, EventContext) by this thread.

Parameters:

fileCreationListener - a file creation listener

clearFileCreationListener

public void clearFileCreationListener()

Clear the file creation listener for this thread.

See Also:

setFileCreationListener(Consumer)

uploadFileset

public ImportProcessPrx uploadFileset(Fileset fs,
                                      ImportSettings settings,
                                      Ice.Current __current)
                               throws ServerError

Return a template based directory path. The path will be created by calling PublicRepositoryI.makeDir(String, boolean, Ice.Current).

Throws:

ServerError

importFileset

public ImportProcessPrx importFileset(Fileset fs,
                                      ImportSettings settings,
                                      Ice.Current __current)
                               throws ServerError

Return a template based directory path. The path will be created by calling PublicRepositoryI.makeDir(String, boolean, Ice.Current).

Specified by:

importFileset in interface _ManagedRepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

importPaths

public ImportProcessPrx importPaths(java.util.List<java.lang.String> paths,
                                    Ice.Current __current)
                             throws ServerError

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

listImports

public java.util.List<ImportProcessPrx> listImports(Ice.Current __current)
                                             throws ServerError

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

Parameters:

__current - The Current object for the invocation.

Throws:

ServerError

listChecksumAlgorithms

public java.util.List<ChecksumAlgorithm> listChecksumAlgorithms(Ice.Current __current)

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

Parameters:

__current - The Current object for the invocation.

suggestChecksumAlgorithm

public ChecksumAlgorithm suggestChecksumAlgorithm(java.util.List<ChecksumAlgorithm> supported,
                                                  Ice.Current __current)

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

__current - The Current object for the invocation.

verifyChecksums

public java.util.List<java.lang.Long> verifyChecksums(java.util.List<java.lang.Long> ids,
                                                      Ice.Current __current)
                                               throws ServerError

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

setChecksumAlgorithm

public java.util.List<java.lang.Long> setChecksumAlgorithm(ChecksumAlgorithm toHasherWrapped,
                                                           java.util.List<java.lang.Long> ids,
                                                           Ice.Current __current)
                                                    throws ServerError

Description copied from interface: _ManagedRepositoryOperations

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 _ManagedRepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

createImportProcess

protected ImportProcessPrx createImportProcess(Fileset fs,
                                               ImportLocation location,
                                               ImportSettings settings,
                                               Ice.Current __current)
                                        throws ServerError

Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.

Throws:

ServerError

createUploadProcess

protected ImportProcessPrx createUploadProcess(Fileset fs,
                                               ImportLocation location,
                                               ImportSettings settings,
                                               Ice.Current __current,
                                               boolean uploadOnly)
                                        throws ServerError

Creating the process will register itself in an appropriate container (i.e. a SessionI or similar) for the current user and therefore this instance no longer needs to worry about the maintenance of the object.

Throws:

ServerError

getReaderClass

protected java.lang.Class<? extends loci.formats.FormatReader> getReaderClass(Fileset fs,
                                                                              Ice.Current __current)

Get the suggested BioFormats Reader for the given Fileset.

Parameters:

fs - a fileset

__current - the current ICE context

Returns:

a reader class, or null if none could be found

commonRoot

protected FsFile commonRoot(java.util.List<FsFile> paths)

From a list of paths, calculate the common root path that all share. In the worst case, that may be "/". May not include the last element, the filename.

Parameters:

paths - some paths

Returns:

the paths' common root

expandTemplateRootOwnedPath

protected FsFile expandTemplateRootOwnedPath(EventContext ctx,
                                             ome.system.ServiceFactory sf)
                                      throws ServerError

Expand the root-owned segment of the template path.

Parameters:

ctx - the event context to apply in expanding terms

sf - the service factory

Returns:

the expanded template path

Throws:

ServerError - if the path could not be expanded

createTemplatePath

protected FsFile createTemplatePath(java.lang.Object consistentData,
                                    Ice.Current __current)
                             throws ServerError

Expand the template path and create its directories with the correct ownership.

Parameters:

consistentData - the object to hash in expanding %hash%

__current - the method invocation context

Returns:

the expanded template path

Throws:

ServerError - if the new path could not be created

createTemplatePath

public FsFile createTemplatePath(java.lang.Object consistentData,
                                 ome.system.EventContext ctx,
                                 ome.system.ServiceFactory sf,
                                 org.hibernate.Session session,
                                 ome.util.SqlAction sql)
                          throws ServerError

Expand the template path and create its directories with the correct ownership. Performs the work of createTemplatePath(Object, Current) except from within an existing transaction.

Parameters:

consistentData - the object to hash in expanding %hash%

ctx - the event context to apply in expanding terms

sf - the service factory

session - the Hibernate session

sql - the JDBC convenience wrapper

Returns:

the expanded template path

Throws:

ServerError - if the new path could not be created

trimPaths

protected ome.services.blitz.repo.ManagedRepositoryI.Paths trimPaths(FsFile basePath,
                                                                     java.util.List<FsFile> fullPaths,
                                                                     java.lang.Class<? extends loci.formats.FormatReader> readerClass)

Trim off the start of long client-side paths.

Parameters:

basePath - the common root

fullPaths - the full paths from the common root down to the filename

readerClass - BioFormats reader for data, may be null

Returns:

possibly trimmed common root and full paths

suggestImportPaths

protected ImportLocation suggestImportPaths(FsFile relPath,
                                            FsFile basePath,
                                            java.util.List<FsFile> paths,
                                            java.lang.Class<? extends loci.formats.FormatReader> reader,
                                            ChecksumAlgorithm checksumAlgorithm,
                                            Ice.Current __current)
                                     throws ServerError

Take a relative path that the user would like to see in his or her upload area, and provide an import location instance whose paths correspond to existing directories corresponding to the sanitized file paths.

Parameters:

relPath - Path parsed from the template

basePath - Common base of all the listed paths ("/my/path")

reader - BioFormats reader for data, may be null

checksumAlgorithm - the checksum algorithm to use in verifying the integrity of uploaded files

Returns:

ImportLocation instance

Throws:

ServerError

makeCheckedDirs

protected void makeCheckedDirs(java.util.LinkedList<CheckedPath> paths,
                               boolean parents,
                               org.hibernate.Session s,
                               ome.system.ServiceFactory sf,
                               ome.util.SqlAction sql,
                               ome.system.EventContext effectiveEventContext)
                        throws ServerError

Checks for the top-level user directory restriction before calling PublicRepositoryI.makeCheckedDirs(LinkedList, boolean, Session, ServiceFactory, SqlAction, EventContext)

Overrides:

makeCheckedDirs in class PublicRepositoryI

Parameters:

paths - Not null, not empty. (Will be emptied by this method.)

parents - "mkdir -p" like flag.

s - the Hibernate session

sf - the service factory

sql - the JDBC convenience wrapper

effectiveEventContext - the event context to apply

Throws:

ServerError

checkPath

protected final CheckedPath checkPath(java.lang.String path,
                                      ChecksumAlgorithm checksumAlgorithm,
                                      Ice.Current curr)
                               throws ValidationException

Description copied from class: PublicRepositoryI

Create a new CheckedPath object based on the given user input. This method is included to allow subclasses a chance to introduce their own CheckedPath implementations.

Overrides:

checkPath in class PublicRepositoryI

Parameters:

path - A path on a repository.

Throws:

ValidationException

checkPath

protected final CheckedPath checkPath(java.lang.String path,
                                      ChecksumAlgorithm checksumAlgorithm)
                               throws ValidationException

Throws:

ValidationException

See Also:

PublicRepositoryI.checkPath(String, ChecksumAlgorithm, Current)

makeDir

public void makeDir(java.lang.String path,
                    boolean parents,
                    org.hibernate.Session session,
                    ome.system.ServiceFactory sf,
                    ome.util.SqlAction sql,
                    ome.system.EventContext effectiveEventContext)
             throws ServerError

Throws:

ServerError

See Also:

PublicRepositoryI.makeDir(CheckedPath, boolean, Session, ServiceFactory, SqlAction, EventContext)