ome.services.blitz.repo

Interface RepositoryDao

All Known Implementing Classes:

RepositoryDaoImpl

public interface RepositoryDao

Method Summary

Modifier and Type	Method and Description
boolean	canUpdate(IObject obj, Ice.Current current) Delegates to IAdmin#canUpdate
void	createOrFixUserDir(java.lang.String uuid, java.util.List<CheckedPath> path, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql) Checks that the given CheckedPath objects exist (via findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
java.util.List<java.lang.Integer>	deleteRepoDeleteLogs(java.util.List<ome.util.SqlAction.DeleteLog> templates, Ice.Current current) Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
int	deleteRepoDeleteLogs(ome.util.SqlAction.DeleteLog template, Ice.Current current) Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
java.util.List<java.lang.Long>	filterFilesByRepository(java.lang.String repo, java.util.List<java.lang.Long> ids, Ice.Current current) Find the original file IDs among those given that are in the given repository.
java.util.List<java.util.List<ome.util.SqlAction.DeleteLog>>	findRepoDeleteLogs(java.util.List<ome.util.SqlAction.DeleteLog> templates, Ice.Current current) As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
java.util.List<ome.util.SqlAction.DeleteLog>	findRepoDeleteLogs(ome.util.SqlAction.DeleteLog template, Ice.Current current) Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
ome.model.core.OriginalFile	findRepoFile(ome.system.ServiceFactory sf, ome.util.SqlAction sql, java.lang.String uuid, CheckedPath checked, java.lang.String mimetype) As findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
OriginalFile	findRepoFile(java.lang.String uuid, CheckedPath checked, java.lang.String mimetype, Ice.Current current) Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery.
ome.model.enums.ChecksumAlgorithm	getChecksumAlgorithm(java.lang.String name, Ice.Current current) Retrieve the checksum algorithm of the given name.
EventContext	getEventContext(Ice.Current current) Look up information for the current session as specified in the ctx field of the current.
FsFile	getFile(long id, Ice.Current current, java.lang.String repoUuid) Get an FsFile object based on its ID.
OriginalFile	getOriginalFile(long fileId, Ice.Current current) Gets the original file instance for a given file ID.
java.util.List<OriginalFile>	getOriginalFiles(java.lang.String repoUuid, CheckedPath checked, Ice.Current current) Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path.
ome.model.core.OriginalFile	getOriginalFileWithHasher(long id, Ice.Current current) Retrieve the original file of the given ID.
ome.api.RawFileStore	getRawFileStore(long fileId, CheckedPath checked, java.lang.String mode, Ice.Current current) Create a RawFileBean (i.e.
java.lang.String	getUserInstitution(long userId, Ice.Current current) Get the current user's institution.
java.lang.String	getUserInstitution(long userId, ome.system.ServiceFactory sf) Get the current user's institution.
java.util.List<Fileset>	loadFilesets(java.util.List<java.lang.Long> ids, Ice.Current current) Load filesets by id.
void	makeDirs(PublicRepositoryI repo, java.util.List<CheckedPath> dirs, boolean parents, Ice.Current c) Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
OriginalFile	register(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, Ice.Current current) Register an OriginalFile object
ome.model.core.OriginalFile	register(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, ome.system.ServiceFactory sf, ome.util.SqlAction sql, org.hibernate.Session session) Like register(String, CheckedPath, String, Ice.Current) but does not create a new transaction.
Fileset	saveFileset(java.lang.String repoUuid, Fileset fs, ChecksumAlgorithm checksumAlgorithm, java.util.List<CheckedPath> paths, Ice.Current current) Fill the various fields of the Fileset and then save the entire instance into the database.
<T extends Job> T	saveJob(T job, Ice.Current current) Create a job from an instance provided by either the client or the server.
void	saveObject(ome.model.IObject object, Ice.Current current) Save the given model object.
RMap	treeList(java.lang.String repoUuid, CheckedPath checked, Ice.Current __current)
void	updateJob(Job job, java.lang.String message, java.lang.String status, Ice.Current current) Set both the message and the status of the given job.

Method Detail

getRawFileStore

ome.api.RawFileStore getRawFileStore(long fileId,
                                     CheckedPath checked,
                                     java.lang.String mode,
                                     Ice.Current current)
                              throws SecurityViolation

Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStoreI for performing internal functions. The primary difference to an instance created via the ServiceFactory is that the RawFileBean.setFileIdWithBuffer(long, FileBuffer) method is called pointing to a non-romio file path, e.g. /OMERO/Files/x.

Parameters:

fileId - ID of an OriginalFile

checked - Not null. Normalized path from the repository.

mode - FileChannel mode, "r", "rw", etc.

Returns:

An instance with RawFileBean.setFileIdWithBuffer(long, FileBuffer) called.

Throws:

SecurityViolation

findRepoFile

OriginalFile findRepoFile(java.lang.String uuid,
                          CheckedPath checked,
                          java.lang.String mimetype,
                          Ice.Current current)
                   throws ServerError

Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery. This will enforce any read security checks.

Parameters:

uuid -

checked -

mimetype -

current -

Returns:

See above.

Throws:

ServerError

findRepoFile

ome.model.core.OriginalFile findRepoFile(ome.system.ServiceFactory sf,
                                         ome.util.SqlAction sql,
                                         java.lang.String uuid,
                                         CheckedPath checked,
                                         java.lang.String mimetype)

As findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.

treeList

RMap treeList(java.lang.String repoUuid,
              CheckedPath checked,
              Ice.Current __current)
       throws ServerError

Throws:

ServerError

createOrFixUserDir

void createOrFixUserDir(java.lang.String uuid,
                        java.util.List<CheckedPath> path,
                        org.hibernate.Session s,
                        ome.system.ServiceFactory sf,
                        ome.util.SqlAction sql)
                 throws ServerError

Checks that the given CheckedPath objects exist (via findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group. If they don't exist, they are created; and if they aren't in the "user" group, they are moved.

Throws:

ServerError

canUpdate

boolean canUpdate(IObject obj,
                  Ice.Current current)

Delegates to IAdmin#canUpdate

Parameters:

obj -

current -

Returns:

See above.

Throws:

an - SecurityViolation if the currentUser is not allowed to access the given file.

filterFilesByRepository

java.util.List<java.lang.Long> filterFilesByRepository(java.lang.String repo,
                                                       java.util.List<java.lang.Long> ids,
                                                       Ice.Current current)

Find the original file IDs among those given that are in the given repository.

Parameters:

repo - a repository UUID

ids - IDs of original files

current - Ice method invocation context

Returns:

those IDs among those given whose original files are in the given repository

getOriginalFile

OriginalFile getOriginalFile(long fileId,
                             Ice.Current current)
                      throws SecurityViolation

Gets the original file instance for a given file ID.

Parameters:

fileId - a file ID

current - applicable ICE context

Returns:

the original file corresponding to the given file ID

Throws:

SecurityViolation - if the query threw a security violation

getOriginalFiles

java.util.List<OriginalFile> getOriginalFiles(java.lang.String repoUuid,
                                              CheckedPath checked,
                                              Ice.Current current)
                                       throws SecurityViolation

Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path. If the directory which they are associated with is not also readable by the current user, then a SecurityViolation will be thrown.

Parameters:

repoUuid - for the repository in question.

checked - normalized path which can be found as the value of OriginalFile.getPath() in the database.

current -

Throws:

SecurityViolation

saveFileset

Fileset saveFileset(java.lang.String repoUuid,
                    Fileset fs,
                    ChecksumAlgorithm checksumAlgorithm,
                    java.util.List<CheckedPath> paths,
                    Ice.Current current)
             throws ServerError

Fill the various fields of the Fileset and then save the entire instance into the database.

Parameters:

repoUuid - for the repository in question.

fs - a user provided Fileset that must minimally have the FilesetEntry objects present with their clientPath set. The rest of the fields will be filled here.

checksumAlgorithm - The algorithm to use.

paths - a List of the same size as the number of entries in fs one per FilesetEntry.

current - Current context

Throws:

ServerError

loadFilesets

java.util.List<Fileset> loadFilesets(java.util.List<java.lang.Long> ids,
                                     Ice.Current current)
                              throws ServerError

Load filesets by id.

Parameters:

ids -

current -

Returns:

See above.

Throws:

ServerError

register

OriginalFile register(java.lang.String repoUuid,
                      CheckedPath checked,
                      java.lang.String mimetype,
                      Ice.Current current)
               throws ServerError

Register an OriginalFile object

Parameters:

repoUuid - uuid of the repository that the given file argument should be registered with. Cannot be null.

checked - Normalized path provided by the repository. Not null.

mimetype - Mimetype for use with the OriginalFile. May be null in which case a default will be chosen.

current - Not null.

Returns:

The OriginalFile with id set (unloaded)

Throws:

ServerError

register

ome.model.core.OriginalFile register(java.lang.String repoUuid,
                                     CheckedPath checked,
                                     java.lang.String mimetype,
                                     ome.system.ServiceFactory sf,
                                     ome.util.SqlAction sql,
                                     org.hibernate.Session session)
                              throws ServerError

Like register(String, CheckedPath, String, Ice.Current) but does not create a new transaction. Instead, the ServiceFactory and SqlAction must be passed in. The returned OriginalFile instance is still connected to Hibernate.

Parameters:

repoUuid -

checked -

mimetype -

sf -

sql -

session -

Returns:

See above.

Throws:

ServerError

getFile

FsFile getFile(long id,
               Ice.Current current,
               java.lang.String repoUuid)

Get an FsFile object based on its ID. Returns null if the file does not exist or does not belong to this repository.

Parameters:

id - database ID of the sought original file

current - current applicable ICE context

repoUuid - the UUID of the repository containing the original file

Returns:

the requested FsFile object

saveJob

<T extends Job> T saveJob(T job,
                          Ice.Current current)
                   throws ServerError

Create a job from an instance provided by either the client or the server. Only those fields which are modifiable by the user will be copied.

Parameters:

job - Not null.

current - Not null.

Returns:

See above.

Throws:

ServerError

updateJob

void updateJob(Job job,
               java.lang.String message,
               java.lang.String status,
               Ice.Current current)
        throws ServerError

Set both the message and the status of the given job.

Parameters:

job - Not null.

message - If null, no modification will be made for the message

status - If null, no modification will be made for the status.

current - Not null.

Throws:

ServerError

getEventContext

EventContext getEventContext(Ice.Current current)

Look up information for the current session as specified in the ctx field of the current.

getUserInstitution

java.lang.String getUserInstitution(long userId,
                                    Ice.Current current)

Get the current user's institution.

Parameters:

userId - the ID of the user whose institution is to be fetched

current - the current ICE method invocation context

Returns:

the institution, may be null

getUserInstitution

java.lang.String getUserInstitution(long userId,
                                    ome.system.ServiceFactory sf)

Get the current user's institution.

Parameters:

userId - the ID of the user whose institution is to be fetched

sf - the service factory to use for the query

Returns:

the institution, may be null

findRepoDeleteLogs

java.util.List<ome.util.SqlAction.DeleteLog> findRepoDeleteLogs(ome.util.SqlAction.DeleteLog template,
                                                                Ice.Current current)

Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.

Parameters:

template - not null.

current - not null.

Returns:

all the rows found which match the non-null fields on templates

findRepoDeleteLogs

java.util.List<java.util.List<ome.util.SqlAction.DeleteLog>> findRepoDeleteLogs(java.util.List<ome.util.SqlAction.DeleteLog> templates,
                                                                                Ice.Current current)

As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.

Parameters:

templates - not null.

current - not null.

Returns:

all the rows found which match the non-null fields on templates

deleteRepoDeleteLogs

int deleteRepoDeleteLogs(ome.util.SqlAction.DeleteLog template,
                         Ice.Current current)

Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.

Parameters:

template - not null.

current - not null.

Returns:

the number of rows deleted

deleteRepoDeleteLogs

java.util.List<java.lang.Integer> deleteRepoDeleteLogs(java.util.List<ome.util.SqlAction.DeleteLog> templates,
                                                       Ice.Current current)

Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.

Parameters:

templates - not null.

current - not null.

Returns:

A list containing the number of rows deleted

makeDirs

void makeDirs(PublicRepositoryI repo,
              java.util.List<CheckedPath> dirs,
              boolean parents,
              Ice.Current c)
       throws ServerError

Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic. Applies the real user's event context when within a PublicRepositoryI.sudo(Current, String).

Throws:

ServerError

getChecksumAlgorithm

ome.model.enums.ChecksumAlgorithm getChecksumAlgorithm(java.lang.String name,
                                                       Ice.Current current)

Retrieve the checksum algorithm of the given name.

Parameters:

name - a checksum algorithm name, must exist

current - Ice method invocation context

Returns:

the corresponding checksum algorithm model object

getOriginalFileWithHasher

ome.model.core.OriginalFile getOriginalFileWithHasher(long id,
                                                      Ice.Current current)

Retrieve the original file of the given ID.

Parameters:

id - the ID of an original file, must exist

current - Ice method invocation context

Returns:

the corresponding original file model object

saveObject

void saveObject(ome.model.IObject object,
                Ice.Current current)

Save the given model object.

Parameters:

object - a model object

current - Ice method invocation context