ome.services.blitz.repo

Class RepositoryDaoImpl

java.lang.Object

ome.services.blitz.repo.RepositoryDaoImpl

All Implemented Interfaces:

RepositoryDao

public class RepositoryDaoImpl
extends java.lang.Object
implements RepositoryDao

DAO class for encapsulating operations related to resource access inside the repository. Methods return types already mapped from Ice. DAO is also used in the form of a mock in unit tests.

Since:

5.0.0

Author:

Blazej Pindelski , Colin Blackburn

Field Summary

Fields

Modifier and Type	Field and Description
protected Executor	executor
protected java.lang.String	fileRepoSecretKey
protected OmeroInterceptor	interceptor
protected Principal	principal
protected Roles	roles
protected Executor	statefulExecutor

Constructor Summary

Constructors

Constructor and Description
RepositoryDaoImpl(Principal principal, Executor executor) Previous constructor which should no longer be used.
RepositoryDaoImpl(Principal principal, Roles roles, Executor executor, Executor statefulExecutor, OmeroInterceptor interceptor, java.lang.String fileRepoSecretKey) Primary constructor which takes all final fields.

Method Summary

Modifier and Type	Method and Description
boolean	canUpdate(omero.model.IObject obj, Ice.Current current) Delegates to IAdmin#canUpdate
protected void	canWriteParentDirectory(ServiceFactory sf, SqlAction sql, java.lang.String repoUuid, CheckedPath parent) Throw a SecurityViolation if the current context cannot write to the parent directory.
void	createOrFixUserDir(java.lang.String repoUuid, java.util.List<CheckedPath> checkedPaths, org.hibernate.Session s, ServiceFactory sf, SqlAction sql) Checks that the given CheckedPath objects exist (via RepositoryDao.findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
protected java.util.List<OriginalFile>	createOriginalFile(ServiceFactory sf, SqlAction sql, java.lang.String repoUuid, java.util.List<CheckedPath> checked, omero.model.ChecksumAlgorithm checksumAlgorithm, java.lang.String mimetype, org.hibernate.Session session) Primary location for creating original files from a CheckedPath instance.
protected Principal	currentUser(Ice.Current __current)
java.util.List<java.lang.Integer>	deleteRepoDeleteLogs(java.util.List<SqlAction.DeleteLog> templates, Ice.Current current) Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
int	deleteRepoDeleteLogs(SqlAction.DeleteLog template, Ice.Current current) Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
protected java.util.Map<java.lang.String,java.lang.String>	fileContext(long fileId, Ice.Current current) Create a String-String map which can be used as the context for a call to Executor.execute based on the group of the file object.
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<SqlAction.DeleteLog>>	findRepoDeleteLogs(java.util.List<SqlAction.DeleteLog> templates, Ice.Current current) As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
java.util.List<SqlAction.DeleteLog>	findRepoDeleteLogs(SqlAction.DeleteLog template, Ice.Current current) Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
OriginalFile	findRepoFile(ServiceFactory sf, SqlAction sql, java.lang.String uuid, CheckedPath checked, java.lang.String mimetype) As RepositoryDao.findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
omero.model.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.
ChecksumAlgorithm	getChecksumAlgorithm(java.lang.String name, Ice.Current current) Retrieve the checksum algorithm of the given name.
omero.sys.EventContext	getEventContext(Ice.Current curr) 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.
omero.model.OriginalFile	getOriginalFile(long repoId, Ice.Current current) Gets the original file instance for a given file ID.
protected java.util.List<OriginalFile>	getOriginalFiles(ServiceFactory sf, SqlAction sql, java.lang.String repoUuid, CheckedPath checked)
java.util.List<omero.model.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.
OriginalFile	getOriginalFileWithHasher(long id, Ice.Current current) Retrieve the original file of the given ID.
RawFileStore	getRawFileStore(long fileId, CheckedPath checked, java.lang.String mode, Ice.Current current) Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStoreI for performing internal functions.
java.lang.String	getUserInstitution(long userId, Ice.Current current) Get the current user's institution.
java.lang.String	getUserInstitution(long userId, ServiceFactory sf) Get the current user's institution.
protected java.util.Map<java.lang.String,java.lang.String>	groupContext(java.lang.Long groupId, Ice.Current current) Creates a copy of the Current.ctx map and if groupId is not null, sets the "omero.group" key to be a string version of the id.
protected void	internalMkdir(CheckedPath file) This method should only be used by the register public method in order to guarantee that the DB is kept in sync with the file system.
java.util.List<omero.model.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 __current) Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
omero.model.OriginalFile	register(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, Ice.Current current) Register an OriginalFile object
OriginalFile	register(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, ServiceFactory sf, SqlAction sql, org.hibernate.Session session) Returns original file object is "live" within the Hibernate session.
omero.model.Fileset	saveFileset(java.lang.String repoUuid, omero.model.Fileset _fs, omero.model.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.
omero.model.Job	saveJob(omero.model.Job job, Ice.Current current) Create a job from an instance provided by either the client or the server.
void	saveObject(IObject object, Ice.Current current) Save the given model object.
omero.RMap	treeList(java.lang.String repoUuid, CheckedPath checked, Ice.Current current)
protected RawFileBean	unwrapRawFileBean(RawFileStore proxy) Loads
void	updateJob(omero.model.Job job, java.lang.String message, java.lang.String status, Ice.Current current) Set both the message and the status of the given job.
protected omero.SecurityViolation	wrapSecurityViolation(SecurityViolation sv)

Methods inherited from class java.lang.Object

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

Field Detail

principal

protected final Principal principal

roles

protected final Roles roles

executor

protected final Executor executor

statefulExecutor

protected final Executor statefulExecutor

interceptor

protected final OmeroInterceptor interceptor

fileRepoSecretKey

protected final java.lang.String fileRepoSecretKey

Constructor Detail

RepositoryDaoImpl

public RepositoryDaoImpl(Principal principal,
                         Roles roles,
                         Executor executor,
                         Executor statefulExecutor,
                         OmeroInterceptor interceptor,
                         java.lang.String fileRepoSecretKey)

Primary constructor which takes all final fields.

RepositoryDaoImpl

public RepositoryDaoImpl(Principal principal,
                         Executor executor)

Previous constructor which should no longer be used. Primarily for simplicity of testing.

Method Detail

unwrapRawFileBean

protected RawFileBean unwrapRawFileBean(RawFileStore proxy)

Loads

Returns:

See above.

wrapSecurityViolation

protected omero.SecurityViolation wrapSecurityViolation(SecurityViolation sv)
                                                 throws omero.SecurityViolation

Throws:

omero.SecurityViolation

getRawFileStore

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

Description copied from interface: RepositoryDao

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.

Specified by:

getRawFileStore in interface RepositoryDao

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:

omero.SecurityViolation

findRepoFile

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

Description copied from interface: RepositoryDao

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.

Specified by:

findRepoFile in interface RepositoryDao

Returns:

See above.

Throws:

omero.ServerError

findRepoFile

public OriginalFile findRepoFile(ServiceFactory sf,
                                 SqlAction sql,
                                 java.lang.String uuid,
                                 CheckedPath checked,
                                 java.lang.String mimetype)

Description copied from interface: RepositoryDao

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

Specified by:

findRepoFile in interface RepositoryDao

treeList

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

Specified by:

treeList in interface RepositoryDao

Throws:

omero.ServerError

createOrFixUserDir

public void createOrFixUserDir(java.lang.String repoUuid,
                               java.util.List<CheckedPath> checkedPaths,
                               org.hibernate.Session s,
                               ServiceFactory sf,
                               SqlAction sql)
                        throws omero.ServerError

Description copied from interface: RepositoryDao

Checks that the given CheckedPath objects exist (via RepositoryDao.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.

Specified by:

createOrFixUserDir in interface RepositoryDao

Throws:

omero.ServerError

canUpdate

public boolean canUpdate(omero.model.IObject obj,
                         Ice.Current current)

Description copied from interface: RepositoryDao

Delegates to IAdmin#canUpdate

Specified by:

canUpdate in interface RepositoryDao

Returns:

See above.

filterFilesByRepository

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

Description copied from interface: RepositoryDao

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

Specified by:

filterFilesByRepository in interface RepositoryDao

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

public omero.model.OriginalFile getOriginalFile(long repoId,
                                                Ice.Current current)
                                         throws omero.SecurityViolation

Description copied from interface: RepositoryDao

Gets the original file instance for a given file ID.

Specified by:

getOriginalFile in interface RepositoryDao

Parameters:

repoId - a file ID

current - applicable ICE context

Returns:

the original file corresponding to the given file ID

Throws:

omero.SecurityViolation - if the query threw a security violation

getOriginalFiles

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

Description copied from interface: RepositoryDao

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.

Specified by:

getOriginalFiles in interface RepositoryDao

Parameters:

repoUuid - for the repository in question.

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

Throws:

omero.SecurityViolation

getOriginalFiles

protected java.util.List<OriginalFile> getOriginalFiles(ServiceFactory sf,
                                                        SqlAction sql,
                                                        java.lang.String repoUuid,
                                                        CheckedPath checked)

saveFileset

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

Description copied from interface: RepositoryDao

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

Specified by:

saveFileset in interface RepositoryDao

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:

omero.ServerError

loadFilesets

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

Description copied from interface: RepositoryDao

Load filesets by id.

Specified by:

loadFilesets in interface RepositoryDao

Returns:

See above.

Throws:

omero.ServerError

register

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

Description copied from interface: RepositoryDao

Register an OriginalFile object

Specified by:

register in interface RepositoryDao

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:

omero.ServerError

register

public OriginalFile register(java.lang.String repoUuid,
                             CheckedPath checked,
                             java.lang.String mimetype,
                             ServiceFactory sf,
                             SqlAction sql,
                             org.hibernate.Session session)
                      throws omero.ServerError

Returns original file object is "live" within the Hibernate session.

Specified by:

register in interface RepositoryDao

Parameters:

repoUuid -

checked -

mimetype -

sf -

sql -

session -

Returns:

See above.

Throws:

omero.ServerError

saveJob

public omero.model.Job saveJob(omero.model.Job job,
                               Ice.Current current)
                        throws omero.ServerError

Description copied from interface: RepositoryDao

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.

Specified by:

saveJob in interface RepositoryDao

Parameters:

job - Not null.

current - Not null.

Returns:

See above.

Throws:

omero.ServerError

updateJob

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

Description copied from interface: RepositoryDao

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

Specified by:

updateJob in interface RepositoryDao

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:

omero.ServerError

makeDirs

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

Description copied from interface: RepositoryDao

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).

Specified by:

makeDirs in interface RepositoryDao

Throws:

omero.ServerError

getFile

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

Description copied from interface: RepositoryDao

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

Specified by:

getFile in interface RepositoryDao

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

findRepoDeleteLogs

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

Description copied from interface: RepositoryDao

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

Specified by:

findRepoDeleteLogs in interface RepositoryDao

Parameters:

template - not null.

current - not null.

Returns:

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

findRepoDeleteLogs

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

Description copied from interface: RepositoryDao

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

Specified by:

findRepoDeleteLogs in interface RepositoryDao

Parameters:

templates - not null.

current - not null.

Returns:

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

deleteRepoDeleteLogs

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

Description copied from interface: RepositoryDao

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

Specified by:

deleteRepoDeleteLogs in interface RepositoryDao

Parameters:

template - not null.

current - not null.

Returns:

the number of rows deleted

deleteRepoDeleteLogs

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

Description copied from interface: RepositoryDao

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

Specified by:

deleteRepoDeleteLogs in interface RepositoryDao

Parameters:

templates - not null.

current - not null.

Returns:

A list containing the number of rows deleted

getEventContext

public omero.sys.EventContext getEventContext(Ice.Current curr)

Description copied from interface: RepositoryDao

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

Specified by:

getEventContext in interface RepositoryDao

getUserInstitution

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

Description copied from interface: RepositoryDao

Get the current user's institution.

Specified by:

getUserInstitution in interface RepositoryDao

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

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

Description copied from interface: RepositoryDao

Get the current user's institution.

Specified by:

getUserInstitution in interface RepositoryDao

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

createOriginalFile

protected java.util.List<OriginalFile> createOriginalFile(ServiceFactory sf,
                                                          SqlAction sql,
                                                          java.lang.String repoUuid,
                                                          java.util.List<CheckedPath> checked,
                                                          omero.model.ChecksumAlgorithm checksumAlgorithm,
                                                          java.lang.String mimetype,
                                                          org.hibernate.Session session)

Primary location for creating original files from a CheckedPath instance. This will use access to the actual File object in order to calculate size, timestamps, etc.

Parameters:

sf -

sql -

repoUuid -

checked -

checksumAlgorithm -

mimetype -

session -

Returns:

See above.

internalMkdir

protected void internalMkdir(CheckedPath file)

This method should only be used by the register public method in order to guarantee that the DB is kept in sync with the file system.

Parameters:

file - the path to ensure exists as a directory

Throws:

ResourceError

canWriteParentDirectory

protected void canWriteParentDirectory(ServiceFactory sf,
                                       SqlAction sql,
                                       java.lang.String repoUuid,
                                       CheckedPath parent)

Throw a SecurityViolation if the current context cannot write to the parent directory.

Parameters:

sf -

sql -

repoUuid -

parent -

currentUser

protected Principal currentUser(Ice.Current __current)

fileContext

protected java.util.Map<java.lang.String,java.lang.String> fileContext(long fileId,
                                                                       Ice.Current current)
                                                                throws omero.SecurityViolation

Create a String-String map which can be used as the context for a call to Executor.execute based on the group of the file object.

Returns:

See above.

Throws:

omero.SecurityViolation - if the file can't be read.

groupContext

protected java.util.Map<java.lang.String,java.lang.String> groupContext(java.lang.Long groupId,
                                                                        Ice.Current current)

Creates a copy of the Current.ctx map and if groupId is not null, sets the "omero.group" key to be a string version of the id.

Parameters:

groupId -

current -

Returns:

See above.

getChecksumAlgorithm

public ChecksumAlgorithm getChecksumAlgorithm(java.lang.String name,
                                              Ice.Current current)

Description copied from interface: RepositoryDao

Retrieve the checksum algorithm of the given name.

Specified by:

getChecksumAlgorithm in interface RepositoryDao

Parameters:

name - a checksum algorithm name, must exist

current - Ice method invocation context

Returns:

the corresponding checksum algorithm model object

getOriginalFileWithHasher

public OriginalFile getOriginalFileWithHasher(long id,
                                              Ice.Current current)

Description copied from interface: RepositoryDao

Retrieve the original file of the given ID.

Specified by:

getOriginalFileWithHasher in interface RepositoryDao

Parameters:

id - the ID of an original file, must exist

current - Ice method invocation context

Returns:

the corresponding original file model object

saveObject

public void saveObject(IObject object,
                       Ice.Current current)

Description copied from interface: RepositoryDao

Save the given model object.

Specified by:

saveObject in interface RepositoryDao

Parameters:

object - a model object

current - Ice method invocation context