ome.services.blitz.repo

Class PublicRepositoryI

java.lang.Object

ome.services.blitz.repo.PublicRepositoryI

All Implemented Interfaces:

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

Direct Known Subclasses:

ManagedRepositoryI

public class PublicRepositoryI
extends Object
implements omero.grid._RepositoryOperations, org.springframework.context.ApplicationContextAware

An implementation of the PublicRepository interface.

Author:

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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PublicRepositoryI.AMD_submit

Field Summary

Fields

Modifier and Type	Field and Description
protected com.google.common.collect.ImmutableList<omero.model.ChecksumAlgorithm>	checksumAlgorithms
protected ChecksumProviderFactory	checksumProviderFactory
protected OmeroContext	context
static String	DIRECTORY_MIMETYPE Mimetype used to connote a directory OriginalFile object.
protected FilePathRestrictions	filePathRestrictions
static String	IMPORT_LOG_MIMETYPE media type for import logs
protected RepositoryDao	repositoryDao
protected ServerFilePathTransformer	serverPaths

Constructor Summary

Constructors

Constructor and Description
PublicRepositoryI(RepositoryDao repositoryDao, ChecksumProviderFactory checksumProviderFactory, String checksumAlgorithmSupported, String pathRules)

Method Summary

Methods

Modifier and Type	Method and Description
protected CheckedPath	checkPath(String path, omero.model.ChecksumAlgorithm checksumAlgorithm, Ice.Current curr) Create a new CheckedPath object based on the given user input.
protected omero.api.RawFileStorePrx	createRepoRFS(CheckedPath checked, String mode, Ice.Current __current) Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
omero.cmd.HandlePrx	deletePaths(String[] files, boolean recursive, boolean force, Ice.Current __current) Delete paths recursively as described in Repositories.ice.
omero.api.RawFileStorePrx	file(String path, String mode, Ice.Current __current)
omero.api.RawFileStorePrx	fileById(long fileId, Ice.Current __current)
boolean	fileExists(String path, Ice.Current __current)
protected omero.model.OriginalFile	findInDb(CheckedPath checked, String mode, Ice.Current current) Find the given path in the DB or create.
protected omero.model.OriginalFile	findOrCreateInDb(CheckedPath checked, String mode, Ice.Current curr)
protected omero.model.OriginalFile	findOrCreateInDb(CheckedPath checked, String mode, String mimetype, Ice.Current curr)
protected Ice.ObjectFactory	getFactory(String id, Ice.Current current)
String	getRepoUuid()
void	initialize(FileMaker fileMaker, Long id, String repoUuid) Called by the internal repository once initialization has taken place.
List<String>	list(String path, Ice.Current __current)
List<omero.model.OriginalFile>	listFiles(String path, Ice.Current __current)
protected Ice.Current	makeAdjustedCurrent(Ice.Current __current)
protected void	makeCheckedDirs(LinkedList<CheckedPath> paths, boolean parents, org.hibernate.Session s, ServiceFactory sf, SqlAction sql, EventContext effectiveEventContext) Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
void	makeDir(CheckedPath checked, boolean parents, org.hibernate.Session s, ServiceFactory sf, SqlAction sql, EventContext effectiveEventContext)
void	makeDir(String path, boolean parents, Ice.Current __current) Create a nested path in the repository.
String	mimetype(String path, Ice.Current __current) Get the mimetype for a file.
protected OriginalFile	persistLogFile(OriginalFile originalFile, Ice.Current current) Deprecated.
omero.api.RawPixelsStorePrx	pixels(String path, Ice.Current __current)
protected void	publishMessage(InternalMessage msg)
omero.model.OriginalFile	register(String path, omero.RString mimetype, Ice.Current __current) Register an OriginalFile using its path
omero.model.OriginalFile	root(Ice.Current __current)
void	setApplicationContext(org.springframework.context.ApplicationContext applicationContext) Set the ApplicationContext that this object runs in.
protected String	stackTraceAsString(Throwable t)
protected PublicRepositoryI.AMD_submit	submitRequest(ServiceFactoryI sf, omero.cmd.Request req, Ice.Current current)
protected Ice.Current	sudo(Ice.Current current, String sessionUuid) Provide a Current like the given one, except with the request context session UUID replaced.
Ice.Object	tie() Wrap the current instance with an TieBase so that it can be turned into a proxy.
omero.RMap	treeList(String path, Ice.Current __current)

Methods inherited from class java.lang.Object

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

Field Detail

DIRECTORY_MIMETYPE

public static final String DIRECTORY_MIMETYPE

Mimetype used to connote a directory OriginalFile object.

See Also:

Constant Field Values

IMPORT_LOG_MIMETYPE

public static final String IMPORT_LOG_MIMETYPE

media type for import logs

See Also:

Constant Field Values

serverPaths

protected ServerFilePathTransformer serverPaths

repositoryDao

protected final RepositoryDao repositoryDao

checksumProviderFactory

protected final ChecksumProviderFactory checksumProviderFactory

checksumAlgorithms

protected final com.google.common.collect.ImmutableList<omero.model.ChecksumAlgorithm> checksumAlgorithms

filePathRestrictions

protected FilePathRestrictions filePathRestrictions

context

protected OmeroContext context

Constructor Detail

PublicRepositoryI

public PublicRepositoryI(RepositoryDao repositoryDao,
                 ChecksumProviderFactory checksumProviderFactory,
                 String checksumAlgorithmSupported,
                 String pathRules)
                  throws omero.ServerError

Throws:

omero.ServerError

Method Detail

initialize

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

Called by the internal repository once initialization has taken place.

Parameters:

fileMaker -

id -

Throws:

omero.ValidationException

tie

public Ice.Object tie()

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.

getRepoUuid

public String getRepoUuid()

root

public omero.model.OriginalFile root(Ice.Current __current)
                              throws omero.ServerError

Specified by:

root in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

fileExists

public boolean fileExists(String path,
                 Ice.Current __current)
                   throws omero.ServerError

Specified by:

fileExists in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

list

public List<String> list(String path,
                Ice.Current __current)
                  throws omero.ServerError

Specified by:

list in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

listFiles

public List<omero.model.OriginalFile> listFiles(String path,
                                       Ice.Current __current)
                                         throws omero.ServerError

Specified by:

listFiles in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

treeList

public omero.RMap treeList(String path,
                  Ice.Current __current)
                    throws omero.ServerError

Specified by:

treeList in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

register

public omero.model.OriginalFile register(String path,
                                omero.RString mimetype,
                                Ice.Current __current)
                                  throws omero.ServerError

Register an OriginalFile using its path

Specified by:

register in interface omero.grid._RepositoryOperations

Parameters:

path - Absolute path of the file to be registered.

mimetype - Mimetype as an RString

__current - ice context.

Returns:

The OriginalFile with id set (unloaded)

Throws:

omero.ServerError

deletePaths

public omero.cmd.HandlePrx deletePaths(String[] files,
                              boolean recursive,
                              boolean force,
                              Ice.Current __current)
                                throws omero.ServerError

Delete paths recursively as described in Repositories.ice. Internally uses treeList(String, Ice.Current) to build the recursive list of files.

Specified by:

deletePaths in interface omero.grid._RepositoryOperations

Parameters:

files - non-null, preferably non-empty list of files to check.

recursive - See Repositories.ice for an explanation

force - See Repositories.ice for an explanation

__current - Non-null ice context.

Throws:

omero.ServerError

mimetype

public String mimetype(String path,
              Ice.Current __current)
                throws omero.ServerError

Get the mimetype for a file.

Specified by:

mimetype in interface omero.grid._RepositoryOperations

Parameters:

path - A path on a repository.

__current - ice context.

Returns:

mimetype

Throws:

omero.ServerError

pixels

public omero.api.RawPixelsStorePrx pixels(String path,
                                 Ice.Current __current)
                                   throws omero.ServerError

Specified by:

pixels in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

file

public omero.api.RawFileStorePrx file(String path,
                             String mode,
                             Ice.Current __current)
                               throws omero.ServerError

Specified by:

file in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

fileById

public omero.api.RawFileStorePrx fileById(long fileId,
                                 Ice.Current __current)
                                   throws omero.ServerError

Specified by:

fileById in interface omero.grid._RepositoryOperations

Throws:

omero.ServerError

findInDb

protected omero.model.OriginalFile findInDb(CheckedPath checked,
                                String mode,
                                Ice.Current current)
                                     throws omero.ServerError

Find the given path in the DB or create. "requiresWrite" is set to true unless the mode is "r". If requiresWrite is true, then the caller needs the file to be modifiable (both on disk and the DB). If this doesn't hold, then a SecurityViolation will be thrown.

Throws:

omero.ServerError

persistLogFile

@Deprecated
protected OriginalFile persistLogFile(OriginalFile originalFile,
                                     Ice.Current current)
                               throws omero.ServerError

Deprecated.

Set the repository of the given original file to be this one. TODO: Should be refactored elsewhere.

Parameters:

originalFileId - the ID of the log file

current - the Ice method invocation context

Throws:

omero.ServerError

findOrCreateInDb

protected omero.model.OriginalFile findOrCreateInDb(CheckedPath checked,
                                        String mode,
                                        Ice.Current curr)
                                             throws omero.ServerError

Throws:

omero.ServerError

findOrCreateInDb

protected omero.model.OriginalFile findOrCreateInDb(CheckedPath checked,
                                        String mode,
                                        String mimetype,
                                        Ice.Current curr)
                                             throws omero.ServerError

Throws:

omero.ServerError

makeAdjustedCurrent

protected Ice.Current makeAdjustedCurrent(Ice.Current __current)

sudo

protected Ice.Current sudo(Ice.Current current,
               String sessionUuid)

Provide a Current like the given one, except with the request context session UUID replaced.

Parameters:

current - an Current instance

sessionUuid - a new session UUID for the instance

Returns:

a new Current instance like the given one but with the new session UUID

createRepoRFS

protected omero.api.RawFileStorePrx createRepoRFS(CheckedPath checked,
                                      String mode,
                                      Ice.Current __current)
                                           throws omero.ServerError,
                                                  omero.InternalException

Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).

Parameters:

checked - The file that will be read. Can't be null, and must have ID set.

mode - The mode for writing. If null, read-only.

__current - The current user's session information.

Returns:

A proxy ready to be returned to the user.

Throws:

omero.ServerError

omero.InternalException

publishMessage

protected void publishMessage(InternalMessage msg)
                       throws omero.ServerError,
                              omero.InternalException

Throws:

omero.ServerError

omero.InternalException

submitRequest

protected PublicRepositoryI.AMD_submit submitRequest(ServiceFactoryI sf,
                                         omero.cmd.Request req,
                                         Ice.Current current)
                                              throws omero.ServerError,
                                                     omero.InternalException

Throws:

omero.ServerError

omero.InternalException

getFactory

protected Ice.ObjectFactory getFactory(String id,
                           Ice.Current current)

makeDir

public void makeDir(String path,
           boolean parents,
           Ice.Current __current)
             throws omero.ServerError

Create a nested path in the repository. Creates each directory in the path is it doen't already exist. Silently returns if the directory already exists.

Specified by:

makeDir in interface omero.grid._RepositoryOperations

Parameters:

path - A path on a repository.

parent - Boolean switch like the "mkdir -p" flag in unix.

__current - ice context.

Throws:

omero.ServerError

makeDir

public void makeDir(CheckedPath checked,
           boolean parents,
           org.hibernate.Session s,
           ServiceFactory sf,
           SqlAction sql,
           EventContext effectiveEventContext)
             throws omero.ServerError

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

Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.

Parameters:

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

parents - "mkdir -p" like flag.

__current -

Throws:

omero.ServerError

setApplicationContext

public void setApplicationContext(org.springframework.context.ApplicationContext applicationContext)
                           throws org.springframework.beans.BeansException

Description copied from interface: org.springframework.context.ApplicationContextAware

Set the ApplicationContext that this object runs in. Normally this call will be used to initialize the object.

Invoked after population of normal bean properties but before an init callback such as InitializingBean.afterPropertiesSet() or a custom init-method. Invoked after ResourceLoaderAware.setResourceLoader(org.springframework.core.io.ResourceLoader), ApplicationEventPublisherAware.setApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher) and MessageSourceAware, if applicable.

Specified by:

setApplicationContext in interface org.springframework.context.ApplicationContextAware

Parameters:

applicationContext - the ApplicationContext object to be used by this object

Throws:

org.springframework.context.ApplicationContextException - in case of context initialization errors

org.springframework.beans.BeansException - if thrown by application context methods

See Also:

BeanInitializationException

checkPath

protected CheckedPath checkPath(String path,
                    omero.model.ChecksumAlgorithm checksumAlgorithm,
                    Ice.Current curr)
                         throws omero.ValidationException

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.

Parameters:

path - A path on a repository.

Throws:

omero.ValidationException

stackTraceAsString

protected String stackTraceAsString(Throwable t)