Package | Description |
---|---|
ome.api |
Contains the central verbs of the Omero System.
|
ome.io.nio |
New Input/Output handling for the OMERO server
This includes interfaces/classes for the input and output handling of data within
the OMERO server.
|
ome.logic |
The central repository of implementations which will be accessible through this server.
|
ome.model.annotations | |
ome.model.core | |
ome.model.fs | |
ome.model.jobs | |
ome.model.roi | |
ome.services |
Base services package for OMERO API services
This includes classes that implement OMERO API services described as interfaces in the
OMERO Common component.
|
ome.services.blitz.repo | |
ome.services.fulltext |
All necessary classes for background indexing of metadata and attached binary
files.
|
ome.services.scripts |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
RawFileStore.save()
Saves the
OriginalFile associated with the service if it has
been modified. |
Modifier and Type | Method and Description |
---|---|
List<OriginalFile> |
IAdmin.getMyUserPhotos()
Retrieve the
OriginalFile object attached to this
user as specified by IAdmin.uploadMyUserPhoto(String, String, byte[]) . |
Modifier and Type | Method and Description |
---|---|
boolean |
OriginalFilesService.exists(OriginalFile file)
Returns whether or not an OriginalFile exists on disk.
|
FileBuffer |
OriginalFilesService.getFileBuffer(OriginalFile file,
String mode)
Returns FileBuffer based on OriginalFile path
|
Modifier and Type | Method and Description |
---|---|
List<OriginalFile> |
AdminImpl.getMyUserPhotos() |
Modifier and Type | Field and Description |
---|---|
protected OriginalFile |
FileAnnotation.file |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
FileAnnotation.getFile()
Many-to-one field ome.model.annotations.FileAnnotation.file (ome.model.core.OriginalFile)
|
OriginalFile |
OriginalFileAnnotationLink.parent() |
Modifier and Type | Method and Description |
---|---|
void |
OriginalFileAnnotationLink.link(OriginalFile parent,
Annotation child) |
void |
FileAnnotation.setFile(OriginalFile file) |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
OriginalFile.newInstance() |
OriginalFile |
PixelsOriginalFileMap.parent() |
OriginalFile |
OriginalFile.proxy() |
Modifier and Type | Method and Description |
---|---|
Iterator<OriginalFile> |
Pixels.linkedOriginalFileIterator()
provides an iterator over the child values of the pixelsFileMaps.
|
List<OriginalFile> |
Pixels.linkedOriginalFileList()
produces a
List -copy of the underlying collection. |
Modifier and Type | Method and Description |
---|---|
Set<PixelsOriginalFileMap> |
Pixels.findPixelsOriginalFileMap(OriginalFile target)
find all ome.model.core.PixelsOriginalFileMap which have the argument as their parent.
|
void |
PixelsOriginalFileMap.link(OriginalFile parent,
Pixels child) |
PixelsOriginalFileMap |
Pixels.linkOriginalFile(OriginalFile addition)
Adds a ome.model.core.PixelsOriginalFileMap to pixelsFileMaps .
|
void |
Pixels.unlinkOriginalFile(OriginalFile removal)
unlinks all ome.model.core.OriginalFile instances from this instance.
|
Modifier and Type | Field and Description |
---|---|
protected OriginalFile |
FilesetEntry.originalFile |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
FilesetEntry.getOriginalFile()
Many-to-one field ome.model.fs.FilesetEntry.originalFile (ome.model.core.OriginalFile)
|
Modifier and Type | Method and Description |
---|---|
void |
FilesetEntry.setOriginalFile(OriginalFile originalFile) |
Constructor and Description |
---|
FilesetEntry(Fileset _fileset,
OriginalFile _originalFile,
String _clientPath) |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
JobOriginalFileLink.child() |
Modifier and Type | Method and Description |
---|---|
Iterator<OriginalFile> |
Job.linkedOriginalFileIterator()
provides an iterator over the parent values of the originalFileLinks.
|
List<OriginalFile> |
Job.linkedOriginalFileList()
produces a
List -copy of the underlying collection. |
Modifier and Type | Method and Description |
---|---|
Set<JobOriginalFileLink> |
Job.findJobOriginalFileLink(OriginalFile target)
find all ome.model.jobs.JobOriginalFileLink which have the argument as their child.
|
void |
JobOriginalFileLink.link(Job parent,
OriginalFile child) |
JobOriginalFileLink |
Job.linkOriginalFile(OriginalFile addition)
Adds a ome.model.jobs.JobOriginalFileLink to originalFileLinks .
|
void |
Job.unlinkOriginalFile(OriginalFile removal)
unlinks all ome.model.core.OriginalFile instances from this instance.
|
Modifier and Type | Field and Description |
---|---|
protected OriginalFile |
Roi.source |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
Roi.getSource()
Many-to-one field ome.model.roi.Roi.source (ome.model.core.OriginalFile)
|
Modifier and Type | Method and Description |
---|---|
void |
Roi.setSource(OriginalFile source) |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
RawFileBean.save() |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
CheckedPath.asOriginalFile(String mimetype)
Creates an
OriginalFile instance for the given
CheckedPath even if it doesn't exist. |
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) |
OriginalFile |
RepositoryDao.getOriginalFileWithHasher(long id,
Ice.Current current)
Retrieve the original file of the given ID.
|
OriginalFile |
RepositoryDaoImpl.getOriginalFileWithHasher(long id,
Ice.Current current) |
protected OriginalFile |
PublicRepositoryI.persistLogFile(OriginalFile originalFile,
Ice.Current current)
Deprecated.
|
OriginalFile |
RepositoryDao.register(String repoUuid,
CheckedPath checked,
String mimetype,
ServiceFactory sf,
SqlAction sql,
org.hibernate.Session session)
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,
org.hibernate.Session session)
Returns original file object is "live" within the Hibernate session.
|
Modifier and Type | Method and Description |
---|---|
protected List<OriginalFile> |
RepositoryDaoImpl.createOriginalFile(ServiceFactory sf,
SqlAction sql,
String repoUuid,
List<CheckedPath> checked,
omero.model.ChecksumAlgorithm checksumAlgorithm,
String mimetype,
org.hibernate.Session session)
Primary location for creating original files from a
CheckedPath
instance. |
protected List<OriginalFile> |
RepositoryDaoImpl.getOriginalFiles(ServiceFactory sf,
SqlAction sql,
String repoUuid,
CheckedPath checked) |
Modifier and Type | Method and Description |
---|---|
protected OriginalFile |
PublicRepositoryI.persistLogFile(OriginalFile originalFile,
Ice.Current current)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
protected void |
BridgeHelper.addContents(org.apache.lucene.document.Document d,
String name,
OriginalFile file,
OriginalFilesService files,
Map<String,FileParser> parsers,
org.hibernate.search.bridge.LuceneOptions opts)
Deprecated.
Second helper method used when parsing files.
|
protected Iterable<Reader> |
BridgeHelper.parse(OriginalFile file,
OriginalFilesService files,
Map<String,FileParser> parsers)
Deprecated.
Attempts to parse the given
OriginalFile . |
Modifier and Type | Method and Description |
---|---|
OriginalFile |
ScriptRepoHelper.addOrReplace(RepoFile repoFile,
Long old) |
protected OriginalFile |
ScriptRepoHelper.addOrReplace(org.hibernate.Session session,
SqlAction sqlAction,
ServiceFactory sf,
RepoFile repoFile,
Long old) |
OriginalFile |
ScriptRepoHelper.load(long id,
boolean check) |
OriginalFile |
ScriptRepoHelper.load(long id,
org.hibernate.Session s,
SqlAction sqlAction,
boolean check) |
OriginalFile |
ScriptRepoHelper.update(RepoFile repoFile,
Long id,
Map<String,String> context) |
Modifier and Type | Method and Description |
---|---|
List<OriginalFile> |
ScriptRepoHelper.loadAll(boolean modificationCheck)
Walks all files in the repository (via
ScriptRepoHelper.iterate() and adds them
if not found in the database. |
List<OriginalFile> |
ScriptRepoHelper.loadAll(boolean modificationCheck,
String mimetype)
Walks all files in the repository (via
ScriptRepoHelper.iterate() and adds them
if not found in the database. |
List<OriginalFile> |
ScriptRepoHelper.loadAll(boolean modificationCheck,
String mimetype,
Principal pp) |
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 |
---|---|
boolean |
ScriptRepoHelper.isInert(OriginalFile f)
Returns
true if the file is an "inert" file e.g. a lut,
false otherwise. |
boolean |
ScriptFileType.setMimetype(OriginalFile ofile)
Sets the mimetype on the given
OriginalFile
if the name field matches the wildcard pattern
for this instance. |
void |
ScriptRepoHelper.setMimetype(OriginalFile ofile) |
Modifier and Type | Method and Description |
---|---|
long |
ScriptRepoHelper.removeMissingFilesFromDb(SqlAction sqlAction,
org.hibernate.Session session,
List<OriginalFile> filesOnDisk)
Given the current files on disk,
ScriptRepoHelper.unregister(Long, SqlAction)
all files which have been removed from disk. |
Version: 5.4.0-ice35-b74
Copyright © 2017 The University of Dundee & Open Microscopy Environment. All Rights Reserved.