Package | Description |
---|---|
ome.formats | |
ome.formats.importer.util | |
ome.logic |
The central repository of implementations which will be accessible through this server.
|
ome.security.basic |
Basic OMERO security contextual classes
Basic classes that provide security context objects necessary to secure the implementation of
the OMERO server on a JBoss platform.
|
ome.services.blitz.fire | |
ome.services.blitz.repo | |
ome.services.fulltext |
All necessary classes for background indexing of metadata and attached binary
files.
|
ome.services.pixeldata | |
ome.services.procs |
Internal process and process management
This includes interfaces and classes that provide thread process management for internal
processes critical to the operation of the OMERO server.
|
ome.services.scripts | |
ome.services.search |
Internal search implementation classes.
|
ome.services.util |
Helper classes to support OMERO service beans
Instead of abstract classes, IOC methods and dependency injection is used to provide service
interception for the Service (binary) bean classes.
|
ome.tools.spring |
OMERO Server tools specific to Spring
Classes/Interfaces that implement AOP, Post-processing injection, session flushing,
and factory management.
|
omero.cmd |
Constructor and Description |
---|
OMEROMetadataStore(ServiceFactory factory,
SqlAction sql)
Creates a new instance.
|
Constructor and Description |
---|
TinyImportFixture(ServiceFactory services) |
Modifier and Type | Method and Description |
---|---|
protected ServiceFactory |
HardWiredInterceptor.getServiceFactory(MethodInvocation mi) |
Modifier and Type | Method and Description |
---|---|
static void |
HardWiredInterceptor.initializeUserAttributes(MethodInvocation mi,
ServiceFactory sf,
Principal pr,
AtomicBoolean reusedSession)
Adds the given environment context objects to the
ReflectiveMethodInvocation.getUserAttributes()
Map for lookup in subclasses |
Modifier and Type | Field and Description |
---|---|
protected ServiceFactory |
BasicSecuritySystem.sf |
Modifier and Type | Method and Description |
---|---|
static BasicSecuritySystem |
BasicSecuritySystem.selfConfigure(SessionManager sm,
ServiceFactory sf,
SessionCache cache)
Simplified factory method which generates all the security primitives
internally.
|
Constructor and Description |
---|
BasicSecuritySystem(OmeroInterceptor interceptor,
SystemTypes sysTypes,
CurrentDetails cd,
SessionManager sessionManager,
Roles roles,
ServiceFactory sf,
TokenHolder tokenHolder,
SecurityFilter filter,
PolicyService policyService)
Main public constructor for this
SecuritySystem implementation. |
Constructor and Description |
---|
AopContextInitializer(ServiceFactory sf,
Principal p,
AtomicBoolean reusedSession) |
Modifier and Type | Method and Description |
---|---|
protected void |
RepositoryDaoImpl.canWriteParentDirectory(ServiceFactory sf,
SqlAction sql,
String repoUuid,
CheckedPath parent)
Throw a
SecurityViolation if the current
context cannot write to the parent directory. |
void |
RepositoryDao.createOrFixUserDir(String uuid,
List<CheckedPath> path,
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. |
void |
RepositoryDaoImpl.createOrFixUserDir(String repoUuid,
List<CheckedPath> checkedPaths,
org.hibernate.Session s,
ServiceFactory sf,
SqlAction sql) |
protected List<OriginalFile> |
RepositoryDaoImpl.createOriginalFile(ServiceFactory sf,
SqlAction sql,
String repoUuid,
List<CheckedPath> checked,
omero.model.ChecksumAlgorithm checksumAlgorithm,
String mimetype)
Primary location for creating original files from a
CheckedPath
instance. |
protected FsFile |
ManagedRepositoryI.expandTemplateRootOwnedPath(omero.sys.EventContext ctx,
ServiceFactory sf)
Expand the root-owned segment of the template path.
|
OriginalFile |
RepositoryDao.findRepoFile(ServiceFactory sf,
SqlAction sql,
String uuid,
CheckedPath checked,
String mimetype)
As
RepositoryDao.findRepoFile(String, CheckedPath, String, Current) but
can be called from within a transaction. |
OriginalFile |
RepositoryDaoImpl.findRepoFile(ServiceFactory sf,
SqlAction sql,
String uuid,
CheckedPath checked,
String mimetype) |
protected List<OriginalFile> |
RepositoryDaoImpl.getOriginalFiles(ServiceFactory sf,
SqlAction sql,
String repoUuid,
CheckedPath checked) |
String |
RepositoryDao.getUserInstitution(long userId,
ServiceFactory sf)
Get the current user's institution.
|
String |
RepositoryDaoImpl.getUserInstitution(long userId,
ServiceFactory sf) |
protected void |
ManagedRepositoryI.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) |
protected void |
PublicRepositoryI.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 |
PublicRepositoryI.makeDir(CheckedPath checked,
boolean parents,
org.hibernate.Session s,
ServiceFactory sf,
SqlAction sql,
EventContext effectiveEventContext) |
OriginalFile |
RepositoryDao.register(String repoUuid,
CheckedPath checked,
String mimetype,
ServiceFactory sf,
SqlAction sql)
Like
RepositoryDao.register(String, CheckedPath, String, Ice.Current) but
does not create a new transaction. |
OriginalFile |
RepositoryDaoImpl.register(String repoUuid,
CheckedPath checked,
String mimetype,
ServiceFactory sf,
SqlAction sql)
Returns original file object is "live" within the Hibernate session.
|
Modifier and Type | Method and Description |
---|---|
Object |
FullTextIndexer.doWork(org.hibernate.Session session,
ServiceFactory sf)
Deprecated.
Runs
FullTextIndexer.doIndexing(FullTextSession) within a Lucene transaction. |
Modifier and Type | Method and Description |
---|---|
Object |
PixelDataHandler.doWork(org.hibernate.Session session,
ServiceFactory sf)
Loads
PixelDataHandler.reps EventLog instances and returns them. |
protected Pixels |
PixelDataHandler.getPixels(Long id,
ServiceFactory sf) |
void |
PixelDataHandler.handleEventLog(EventLog eventLog,
org.hibernate.Session session,
ServiceFactory sf)
Handles only single elements from the
PersistentEventLogLoader
in order to keep transactions short and safe. |
boolean |
PixelDataHandler.process(Long id,
ServiceFactory sf,
org.hibernate.Session s)
Here we assume that our log loader will only return
us the proper types, since we are using the specific
type defined in this package.
|
Modifier and Type | Method and Description |
---|---|
List<Job> |
ProcessManager.Work.doWork(org.hibernate.Session session,
ServiceFactory sf) |
protected Job |
ProcessManager.Work.job(ServiceFactory sf,
long id) |
void |
ProcessManager.Work.startProcess(ServiceFactory sf,
long jobId) |
Modifier and Type | Method and Description |
---|---|
protected OriginalFile |
ScriptRepoHelper.addOrReplace(org.hibernate.Session session,
SqlAction sqlAction,
ServiceFactory sf,
RepoFile repoFile,
Long old) |
omero.model.ScriptJob |
ScriptFinder.createJob(ServiceFactory sf)
Returns a fresh (unsaved)
ScriptJob which can be passed to
acquireProcessor for background processing. |
omero.model.OriginalFileI |
ScriptFinder.getFile(ServiceFactory sf) |
protected List<OriginalFile> |
ScriptFinder.loadScripts(ServiceFactory sf,
Parameters p)
Load all scripts that match the name, hash, and format for script
|
Modifier and Type | Method and Description |
---|---|
Object |
AnnotatedWith.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Object |
Complement.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Object |
FullText.doWork(org.hibernate.Session s,
ServiceFactory sf) |
Object |
HqlQuery.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Object |
Intersection.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Object |
SimilarTerms.doWork(org.hibernate.Session s,
ServiceFactory sf) |
Object |
TagsAndGroups.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Object |
Union.doWork(org.hibernate.Session session,
ServiceFactory sf) |
Modifier and Type | Method and Description |
---|---|
X |
Executor.Work.doWork(org.hibernate.Session session,
ServiceFactory sf)
Work method.
|
Modifier and Type | Class and Description |
---|---|
class |
InternalServiceFactory
subclass of ome.system.ServiceFactory which retrieves unmanaged ("internal")
service- instances. |
class |
ManagedServiceFactory
subclass of ome.system.ServiceFactory which retrieves managed
service- instances. |
Modifier and Type | Method and Description |
---|---|
ServiceFactory |
Helper.getServiceFactory() |
Modifier and Type | Method and Description |
---|---|
List<Object> |
HandleI.steps(SqlAction sql,
org.hibernate.Session session,
ServiceFactory sf) |
Constructor and Description |
---|
Helper(omero.cmd.Request request,
omero.cmd.Status status,
SqlAction sql,
org.hibernate.Session session,
ServiceFactory sf) |
Version: 5.3.5-ice35-b73
Copyright © 2017 The University of Dundee & Open Microscopy Environment. All Rights Reserved.