ome.services.blitz.repo

Class ManagedRepositoryI

java.lang.Object

ome.services.blitz.repo.PublicRepositoryI

ome.services.blitz.repo.ManagedRepositoryI

All Implemented Interfaces:

omero.grid._ManagedRepositoryOperations, omero.grid._RepositoryOperations, org.springframework.context.ApplicationContextAware

public class ManagedRepositoryI
extends PublicRepositoryI
implements omero.grid._ManagedRepositoryOperations

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

Since:

5.0

Author:

Colin Blackburn , Josh Moore, josh at glencoesoftware.com, m.t.b.carroll@dundee.ac.uk

Nested Class Summary

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

PublicRepositoryI.AMD_submit

Field Summary

Fields

Modifier and Type	Field and 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 and Description
ManagedRepositoryI(String template, RepositoryDao dao) Creates a ProcessContainer internally that will not be managed by background threads.
ManagedRepositoryI(String template, RepositoryDao dao, ProcessContainer processes, ChecksumProviderFactory checksumProviderFactory, String checksumAlgorithmSupported, String pathRules, String rootSessionUuid, Roles roles, Set<String> managedRepoUuids)

Method Summary

Modifier and Type	Method and Description
protected FsFile	commonRoot(List<FsFile> paths) From a list of paths, calculate the common root path that all share.
protected omero.grid.ImportProcessPrx	createImportProcess(omero.model.Fileset fs, omero.grid.ImportLocation location, omero.grid.ImportSettings settings, Ice.Current __current) 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.
protected FsFile	createTemplatePath(Object consistentData, Ice.Current __current) Expand the template path and create its directories with the correct ownership.
protected omero.grid.ImportProcessPrx	createUploadProcess(omero.model.Fileset fs, omero.grid.ImportLocation location, omero.grid.ImportSettings settings, Ice.Current __current, boolean uploadOnly) 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.
protected FsFile	expandTemplateRootOwnedPath(omero.sys.EventContext ctx, ServiceFactory sf) Expand the root-owned segment of the template path.
protected Class<? extends FormatReader>	getReaderClass(omero.model.Fileset fs, Ice.Current __current) Get the suggested BioFormats Reader for the given Fileset.
omero.grid.ImportProcessPrx	importFileset(omero.model.Fileset fs, omero.grid.ImportSettings settings, Ice.Current __current) Return a template based directory path.
omero.grid.ImportProcessPrx	importPaths(List<String> paths, Ice.Current __current)
void	initialize(FileMaker fileMaker, Long id, String repoUuid) Called by the internal repository once initialization has taken place.
List<omero.model.ChecksumAlgorithm>	listChecksumAlgorithms(Ice.Current __current)
List<omero.grid.ImportProcessPrx>	listImports(Ice.Current __current)
protected void	makeCheckedDirs(LinkedList<CheckedPath> paths, boolean parents, org.hibernate.Session s, ServiceFactory sf, SqlAction sql, EventContext effectiveEventContext) Checks for the top-level user directory restriction before calling PublicRepositoryI.makeCheckedDirs(LinkedList, boolean, Session, ServiceFactory, SqlAction, ome.system.EventContext)
List<Long>	setChecksumAlgorithm(omero.model.ChecksumAlgorithm toHasherWrapped, List<Long> ids, Ice.Current __current)
omero.model.ChecksumAlgorithm	suggestChecksumAlgorithm(List<omero.model.ChecksumAlgorithm> supported, Ice.Current __current)
protected omero.grid.ImportLocation	suggestImportPaths(FsFile relPath, FsFile basePath, List<FsFile> paths, Class<? extends FormatReader> reader, omero.model.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, List<FsFile> fullPaths, Class<? extends FormatReader> readerClass) Trim off the start of long client-side paths.
omero.grid.ImportProcessPrx	uploadFileset(omero.model.Fileset fs, omero.grid.ImportSettings settings, Ice.Current __current) Return a template based directory path.
List<Long>	verifyChecksums(List<Long> ids, Ice.Current __current)

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

checkPath, createRepoRFS, deletePaths, file, fileById, fileExists, findInDb, findOrCreateInDb, findOrCreateInDb, getFactory, getRepoUuid, list, listFiles, makeAdjustedCurrent, makeDir, makeDir, mimetype, persistLogFile, pixels, publishMessage, register, root, setApplicationContext, stackTraceAsString, 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, pixels, register, root, treeList

Field Detail

templateRoot

protected FsFile templateRoot

Constructor Detail

ManagedRepositoryI

public ManagedRepositoryI(String template,
                          RepositoryDao dao)
                   throws Exception

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

Parameters:

template -

dao -

Throws:

Exception

ManagedRepositoryI

public ManagedRepositoryI(String template,
                          RepositoryDao dao,
                          ProcessContainer processes,
                          ChecksumProviderFactory checksumProviderFactory,
                          String checksumAlgorithmSupported,
                          String pathRules,
                          String rootSessionUuid,
                          Roles roles,
                          Set<String> managedRepoUuids)
                   throws omero.ServerError

Throws:

omero.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,
                       Long id,
                       String repoUuid)
                throws omero.ValidationException

Description copied from class: PublicRepositoryI

Called by the internal repository once initialization has taken place.

Overrides:

initialize in class PublicRepositoryI

Throws:

omero.ValidationException

uploadFileset

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

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

Throws:

omero.ServerError

importFileset

public omero.grid.ImportProcessPrx importFileset(omero.model.Fileset fs,
                                                 omero.grid.ImportSettings settings,
                                                 Ice.Current __current)
                                          throws omero.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 omero.grid._ManagedRepositoryOperations

Throws:

omero.ServerError

importPaths

public omero.grid.ImportProcessPrx importPaths(List<String> paths,
                                               Ice.Current __current)
                                        throws omero.ServerError

Specified by:

importPaths in interface omero.grid._ManagedRepositoryOperations

Throws:

omero.ServerError

listImports

public List<omero.grid.ImportProcessPrx> listImports(Ice.Current __current)
                                              throws omero.ServerError

Specified by:

listImports in interface omero.grid._ManagedRepositoryOperations

Throws:

omero.ServerError

listChecksumAlgorithms

public List<omero.model.ChecksumAlgorithm> listChecksumAlgorithms(Ice.Current __current)

Specified by:

listChecksumAlgorithms in interface omero.grid._ManagedRepositoryOperations

suggestChecksumAlgorithm

public omero.model.ChecksumAlgorithm suggestChecksumAlgorithm(List<omero.model.ChecksumAlgorithm> supported,
                                                              Ice.Current __current)

Specified by:

suggestChecksumAlgorithm in interface omero.grid._ManagedRepositoryOperations

verifyChecksums

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

Specified by:

verifyChecksums in interface omero.grid._ManagedRepositoryOperations

Throws:

omero.ServerError

setChecksumAlgorithm

public List<Long> setChecksumAlgorithm(omero.model.ChecksumAlgorithm toHasherWrapped,
                                       List<Long> ids,
                                       Ice.Current __current)
                                throws omero.ServerError

Specified by:

setChecksumAlgorithm in interface omero.grid._ManagedRepositoryOperations

Throws:

omero.ServerError

createImportProcess

protected omero.grid.ImportProcessPrx createImportProcess(omero.model.Fileset fs,
                                                          omero.grid.ImportLocation location,
                                                          omero.grid.ImportSettings settings,
                                                          Ice.Current __current)
                                                   throws omero.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:

omero.ServerError

createUploadProcess

protected omero.grid.ImportProcessPrx createUploadProcess(omero.model.Fileset fs,
                                                          omero.grid.ImportLocation location,
                                                          omero.grid.ImportSettings settings,
                                                          Ice.Current __current,
                                                          boolean uploadOnly)
                                                   throws omero.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:

omero.ServerError

getReaderClass

protected Class<? extends FormatReader> getReaderClass(omero.model.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(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(omero.sys.EventContext ctx,
                                             ServiceFactory sf)
                                      throws omero.ServerError

Expand the root-owned segment of the template path.

Parameters:

ctx - the event context to apply in expanding terms

sf - the service factory which to perform queries

Returns:

the expanded template path

Throws:

omero.ServerError - if the path could not be expanded

createTemplatePath

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

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

Parameters:

consistentData - the object to hash in expanding %hash%

__current - the current ICE method invocation context

Returns:

the expanded template path

Throws:

omero.ServerError - if the new path could not be created

trimPaths

protected ome.services.blitz.repo.ManagedRepositoryI.Paths trimPaths(FsFile basePath,
                                                                     List<FsFile> fullPaths,
                                                                     Class<? extends 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 omero.grid.ImportLocation suggestImportPaths(FsFile relPath,
                                                       FsFile basePath,
                                                       List<FsFile> paths,
                                                       Class<? extends FormatReader> reader,
                                                       omero.model.ChecksumAlgorithm checksumAlgorithm,
                                                       Ice.Current __current)
                                                throws omero.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:

omero.ServerError

makeCheckedDirs

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

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

Throws:

omero.ServerError