Package ome.services.blitz.repo

Class PublicRepositoryI

java.lang.Object

ome.services.blitz.repo.PublicRepositoryI

All Implemented Interfaces:

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

Direct Known Subclasses:

ManagedRepositoryI

public class PublicRepositoryI
extends java.lang.Object
implements _RepositoryOperations, org.springframework.context.ApplicationContextAware

An implementation of the PublicRepository interface.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	PublicRepositoryI.AMD_submit

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	Description
PublicRepositoryI(RepositoryDao repositoryDao, ome.util.checksum.ChecksumProviderFactory checksumProviderFactory, java.lang.String checksumAlgorithmSupported, java.lang.String pathRules)

Method Summary

Modifier and Type	Method	Description
protected CheckedPath	checkPath(java.lang.String path, ChecksumAlgorithm checksumAlgorithm, Ice.Current curr)	Create a new CheckedPath object based on the given user input.
protected RawFileStorePrx	createRepoRFS(CheckedPath checked, java.lang.String mode, Ice.Current __current)	Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
HandlePrx	deletePaths(java.lang.String[] files, boolean recursive, boolean force, Ice.Current __current)	Delete paths recursively as described in Repositories.ice.
RawFileStorePrx	file(java.lang.String path, java.lang.String mode, Ice.Current __current)	Returns a special RawFileStore which permits only the operations set out in the options string ""wb"", ""a+"", etc.
RawFileStorePrx	fileById(long fileId, Ice.Current __current)
boolean	fileExists(java.lang.String path, Ice.Current __current)	Returns true if the file or path exists within the repository.
protected OriginalFile	findInDb(CheckedPath checked, java.lang.String mode, Ice.Current current)	Find the given path in the DB or create.
protected OriginalFile	findOrCreateInDb(CheckedPath checked, java.lang.String mode, Ice.Current curr)
protected OriginalFile	findOrCreateInDb(CheckedPath checked, java.lang.String mode, java.lang.String mimetype, Ice.Current curr)
protected Ice.ObjectFactory	getFactory(java.lang.String id, Ice.Current current)
java.lang.String	getRepoUuid()
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<java.lang.String>	list(java.lang.String path, Ice.Current __current)	Returns a set of strings naming the files and directories in the directory denoted by an abstract pathname.
java.util.List<OriginalFile>	listFiles(java.lang.String path, Ice.Current __current)	Returns an array of abstract pathname objects denoting the files in the directory denoted by an abstract pathname.
protected Ice.Current	makeAdjustedCurrent(Ice.Current __current)
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)	Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
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, java.util.function.Consumer<CheckedPath> fileCreationListener)	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(java.lang.String path, boolean parents, Ice.Current current)	Create a nested path in the repository.
void	makeDir(CheckedPath checked, boolean parents, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext)
java.lang.String	mimetype(java.lang.String path, Ice.Current __current)	Get the mimetype for a file.
protected ome.model.core.OriginalFile	persistLogFile(ome.model.core.OriginalFile originalFile, Ice.Current current)	Deprecated.
protected void	publishMessage(ome.util.messages.InternalMessage msg)
OriginalFile	register(java.lang.String path, RString mimetype, Ice.Current __current)	Register an OriginalFile using its path
OriginalFile	root(Ice.Current __current)	Return the OriginalFile descriptor for this Repository.
java.lang.String	rootPath(org.hibernate.Session session, ome.system.ServiceFactory serviceFactory)
void	setApplicationContext(org.springframework.context.ApplicationContext applicationContext)
protected java.lang.String	stackTraceAsString(java.lang.Throwable t)
protected PublicRepositoryI.AMD_submit	submitRequest(ServiceFactoryI sf, Request req, Ice.Current current)
protected PublicRepositoryI.AMD_submit	submitRequest(ServiceFactoryI sf, Request req, Ice.Current current, ome.services.util.Executor.Priority priority)
protected Ice.Current	sudo(Ice.Current current, java.lang.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.
RMap	treeList(java.lang.String path, Ice.Current __current)	Similar to list but recursive and returns only primitive values for the file at each location.

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 java.lang.String DIRECTORY_MIMETYPE

Mimetype used to connote a directory OriginalFile object.

See Also:

Constant Field Values

IMPORT_LOG_MIMETYPE

public static final java.lang.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 ome.util.checksum.ChecksumProviderFactory checksumProviderFactory

checksumAlgorithms

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

filePathRestrictions

protected FilePathRestrictions filePathRestrictions

context

protected ome.system.OmeroContext context

Constructor Detail

PublicRepositoryI

public PublicRepositoryI(RepositoryDao repositoryDao,
                         ome.util.checksum.ChecksumProviderFactory checksumProviderFactory,
                         java.lang.String checksumAlgorithmSupported,
                         java.lang.String pathRules)
                  throws ServerError

Throws:

ServerError

Method Detail

initialize

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

Called by the internal repository once initialization has taken place.

Parameters:

fileMaker -

id -

Throws:

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 java.lang.String getRepoUuid()

root

public OriginalFile root(Ice.Current __current)
                  throws ServerError

Description copied from interface: _RepositoryOperations

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 _RepositoryOperations

Parameters:

__current - The Current object for the invocation.

Throws:

ServerError

fileExists

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

Description copied from interface: _RepositoryOperations

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 _RepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

list

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

Description copied from interface: _RepositoryOperations

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

Specified by:

list in interface _RepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

listFiles

public java.util.List<OriginalFile> listFiles(java.lang.String path,
                                              Ice.Current __current)
                                       throws ServerError

Description copied from interface: _RepositoryOperations

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 _RepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

treeList

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

Description copied from interface: _RepositoryOperations

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 _RepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

rootPath

public java.lang.String rootPath(org.hibernate.Session session,
                                 ome.system.ServiceFactory serviceFactory)
                          throws ServerError

Parameters:

session - the Hibernate session

serviceFactory - the service factory

Returns:

the filesystem path set for this repository's root directory

Throws:

ServerError - if the root path could not be retrieved

register

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

Register an OriginalFile using its path

Specified by:

register in interface _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:

ServerError

deletePaths

public HandlePrx deletePaths(java.lang.String[] files,
                             boolean recursive,
                             boolean force,
                             Ice.Current __current)
                      throws 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 _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:

ServerError

mimetype

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

Get the mimetype for a file.

Specified by:

mimetype in interface _RepositoryOperations

Parameters:

path - A path on a repository.

__current - ice context.

Returns:

mimetype

Throws:

ServerError

file

public RawFileStorePrx file(java.lang.String path,
                            java.lang.String mode,
                            Ice.Current __current)
                     throws ServerError

Description copied from interface: _RepositoryOperations

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 _RepositoryOperations

__current - The Current object for the invocation.

Throws:

ServerError

fileById

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

Specified by:

fileById in interface _RepositoryOperations

Throws:

ServerError

findInDb

protected OriginalFile findInDb(CheckedPath checked,
                                java.lang.String mode,
                                Ice.Current current)
                         throws 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:

ServerError

persistLogFile

@Deprecated
protected ome.model.core.OriginalFile persistLogFile(ome.model.core.OriginalFile originalFile,
                                                     Ice.Current current)
                                              throws ServerError

Deprecated.

Set the repository of the given original file to be this one.

Parameters:

originalFile - the ID of the log file

current - the Ice method invocation context

Throws:

ServerError

findOrCreateInDb

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

Throws:

ServerError

findOrCreateInDb

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

Throws:

ServerError

makeAdjustedCurrent

protected Ice.Current makeAdjustedCurrent(Ice.Current __current)

sudo

protected Ice.Current sudo(Ice.Current current,
                           java.lang.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 RawFileStorePrx createRepoRFS(CheckedPath checked,
                                        java.lang.String mode,
                                        Ice.Current __current)
                                 throws ServerError,
                                        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:

ServerError

InternalException

publishMessage

protected void publishMessage(ome.util.messages.InternalMessage msg)
                       throws ServerError,
                              InternalException

Throws:

ServerError

InternalException

submitRequest

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

Throws:

ServerError

InternalException

submitRequest

protected PublicRepositoryI.AMD_submit submitRequest(ServiceFactoryI sf,
                                                     Request req,
                                                     Ice.Current current,
                                                     ome.services.util.Executor.Priority priority)
                                              throws ServerError,
                                                     InternalException

Throws:

ServerError

InternalException

getFactory

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

makeDir

public void makeDir(java.lang.String path,
                    boolean parents,
                    Ice.Current current)
             throws 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 _RepositoryOperations

Parameters:

path - A path on a repository.

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

current - ice context.

Throws:

ServerError

makeDir

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

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

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.

s - the Hibernate session

sf - the service factory

sql - the JDBC convenience wrapper

effectiveEventContext - the event context to apply

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,
                               java.util.function.Consumer<CheckedPath> fileCreationListener)
                        throws 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.

s - the Hibernate session

sf - the service factory

sql - the JDBC convenience wrapper

effectiveEventContext - the event context to apply

fileCreationListener - the file creation listener to notify of new directories being created

Throws:

ServerError

setApplicationContext

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

Specified by:

setApplicationContext in interface org.springframework.context.ApplicationContextAware

Throws:

org.springframework.beans.BeansException

checkPath

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

ValidationException

stackTraceAsString

protected java.lang.String stackTraceAsString(java.lang.Throwable t)