Import under OMERO.fs
The OMERO 5 release introduces OMERO.fs, a new way of storing files in the
OMERO binary repository and thus a new method of importing images to the
server.
In previous versions of OMERO the import process was very much
client-centered. When importing an image the client pushed pixel data,
metadata and, optionally, original image files to the OMERO server. With
the advent of OMERO 5, OMERO.fs allows the pixels to be accessed
directly from the original image files. This means that much of the
import process can now take place on the server once the original image
files have been uploaded.
This page looks at the implications for the developer writing import clients.
A broad description of the import workflow is followed by some of the model
changes needed to facilitate this workflow. The current API sequence is then
introduced before looking at server-side classes and sequence. Finally, the
configuration required for OMERO.fs is specified.
Import overview
The broad import workflow comprises selecting a file or set of files to be
imported client-side. Using Bio-Formats on the client this selection is
resolved into a number of import candidates. Here an import candidate is a
file or set of files that represents a single image, a multi-image set or a
plate. Each import candidate, which may be one file or several files, is then
treated as Fileset for import. The import of each Fileset is then
undertaken by the client in two stages: upload and server-side import.
A Fileset is uploaded to the server into a location determined by the
server, multiple Filesets may be uploaded in parallel by a client. A
checksum is calculated before upload by the client and after upload by the
server. If these checksums match then the client triggers a server-side
import. The client can then move on to doing other work and leave the import
to complete on the server.
Once the Fileset is on the server and an import has been initiated by the
client all processing then takes place on the server. The server then uses
Bio-Formats to extract and store the metadata, calculate the minimum and
maximum pixel values and do other import processing.
Model description
See acquisition.ome.xml.
- ome.model.fs.Fileset
- Represents a group of files which are considered to belong together.
- In the future the client may upload a single “import set” that is
subsequently resolved by Bio-Formats into multiple filesets on the
server.
- Also links to multiple ome.model.jobs.Job instances.
- Links to the image objects that are created during import.
- ome.model.jobs.Job subclasses
- Each one represents some action which takes place server-side on the
Fileset.
- For the standard sequence described above, the first will always be an
UploadJob which contains version info from the client. If the
files were not uploaded however, this may not be the case. Then a
MetadataImportJob follows, which is the basic import.
- Other jobs may be necessary for regular usage (PixelDataJob,
IndexingJob, etc.). Later jobs may also be added like a
re-parse job, a re-check of the hashes to detect corruption, or an
archive job.
- For job definitions, see jobs.ome.xml.
- Some subclasses have a versionInfo property for storing
a snapshot of process information along with software
versions. Most important for knowing how files were parsed, therefore
when using importPaths, a “synthetic” version info might be created
to say that these were just uploaded blindly.
- ome.model.fs.FilesetEntry
- Link from a Fileset to exactly one ome.model.core.OriginalFile
- Critically, it also contains the original absolute client path of that
file.
API sequence
- Choose which files to import by either:
- ImportLibrary and friends (Java only)
- listing all files (not directories) manually.
- Choose a ManagedRepositoryPrx from
SharedResourcesPrx.repositories().
- Call either:
- ImportLibrary.importImage() which calls
ManagedRepositoryPrx.importFilesets(Fileset, ImportSettings), or
- directly use ManagedRepositoryPrx.importPaths(StringSet).
- Receive an ImportProcessPrx.
- For each FileEntry in the FileSet or each path in the StringSet
(in order), call ImportProcessPrx.getUploader() and receive a
RawFileStorePrx.
- Upload the file via RawFileStorePrx.write() while reading the files
locally to write, be sure to calculate the checksum.
- Pass a list of checksums (in order) to
ImportProcessPrx.verifyUpload(StringSet). If the hashes match, receive a
HandlePrx. Otherwise an exception is thrown.
At this point, the client should be able to disconnect and the rest of the
import should happen independently.
- Create an CmdCallbackI that wraps the HandlePrx and wait for
successful completion.
At this point, the main metadata import is finished, but background processing
may still be occurring. Handles for the background processing will
also be returned.
Server-side classes/concepts
AbstractRepositoryI and all of its subclasses are implementations of the
InternalRepository API. These objects are for internal use only and should
never be accessible by the clients. Each instance is initialized with a
directory which the servant attempts to “acquire” (i.e. grab a lock file).
Once it does so, it is the serving repository.
Each internal repository provides a public view which in turn provides the
Repository API. All method calls assume Unix-style strings, which are
guaranteed by CheckedPath, a loose wrapper around java.io.File.
CheckedPath objects along with the active Ice.Current instance are passed
to the RepositoryDao interface, which provides database access for all
repositories. Access to raw IO is provided by the RepoRawFileStoreI
servant, which wraps a RawFileBean.
The ManagedRepository implementation is responsible for import and
enforces further constraints (beyond those of CheckedPath) on where and what
files are created. Most importantly, the omero.fs.repo.path template
value is expanded and pre-pended to all uploads. A further responsibility of
the ManagedRepository is to maintain a list of all currently running
ManagedImportProcessI, each of which is held in the ProcessContainer.
These ManagedImportProcessI instances further wrap RepoRawFileStoreI
instances with a subclass, ManagedRawFileStoreI.
For file import through ManagedRepository.importFileset, although hasher is
nullable ordinarily, it will be set through the mandatory
ImportSettings.checksumAlgorithm property.
ManagedRepository.listChecksumAlgorithms lists the hashers supported by the
server. ManagedRepository.suggestChecksumAlgorithm helps the client and
server to negotiate a mutually acceptable algorithm, as in
ImportLibrary.createImport; the result is affected by the server’s
configuration setting for omero.checksum.supported. ImportLibrary
calculates each file’s hash using hashers obtained through
ChecksumProviderFactory.getProvider. In fetching OriginalFile objects by HQL
through the Query Service one needs JOIN FETCH on the hasher property to
read the hasher’s name.
Server-side sequence
NB: Server-side ImportLibrary is no longer being used. That logic is
currently moved to ManagedImportRequestI. This may not be the best
location. Further, several other layers might also be collapsible, like
OMEROMetadataStore which is currently accessible as a “hidden”
service MetadataStorePrx. Here, “hidden” means that it is not
directly retrievable from ServiceFactoryPrx.
- ManagedRepositoryI.importPaths()
- reuses ImportContainer.fillData() to create an ImportSettings
and a Fileset and then calls importFileset(Fileset, ImportSettings)
- ManagedRepositoryI.importFileset()
- determines an ImportLocation calling PublicRepositoryI.makeDir()
where necessary.
- createImportProcess creates a ManagedImportProcessI, registers it,
and returns it.
- After this, the repository is only responsible for periodically having the
ping and eventually the shutdown method called, via ProcessContainer.
- ManagedImportProcessI.getUploader()
- creates a new RepositoryRawFileStoreI for each file in the
paths/fileset.
- Once close() is called on this instance, closeCalled(int i) will
be called on the import process and the instance will be removed.
- If getUploader() is called again, then a new file store will be
created.
- ManagedImportProcessI.verifyUpload()
- If all hashes match, then a ManagedImportRequestI instance is created
and submitted to omero.cmd.SessionI.submit_async() for background
processing. The client can wait for the returned omero.cmd.HandlePrx
to finish by using a CmdCallbackI.
- At this point, the ImportProcessPrx can be closed as well as the
entire client and the import would still continue. Only if
HandlePrx.cancel() is called, will the import be aborted.
- QUESTION: How to handle rollback at this point?
- ManagedImportRequestI.init (within transaction)
- Registry.getInternalServiceFactory() grabs a ServiceFactoryPrx
without the need for an omero.client instance.
- OMEROWrapper and a OMEROMetadataStoreClient are created with this
connection.
- Some other basic configuration takes place.
- ManagedImportRequest.step() (N times, each within same transaction as
init())
- NB: it may later make more sense for this bit to happen in a separate
process.
- At the moment, 5 steps are hard-coded. Each performing roughly the same
amount of work. Some of these may later be done in the background.
- importMetadata() calls store.saveToDB(), which calls
MetadataStorePrx.saveToDb(), a remote call. This could possibly be
inlined.
- generateThumbnails() calls
store.resetDefaultsAndGenerateThumbnails(), another remote call,
which could also be inlined.
- pixelData() calls store.setPixelsParams(), updatePixels(),
and populateMinMax(). Min/Max especially should be backgrounded.
- Finally, store.launchProcessing() is called, which should remain,
but could also be inlined. The returned script processes could be
returned in the ImportResponse.
- Return appropriate values.
- notifyObservers() currently does nothing, since this was client-side
functionality in ImportLibrary. This needs to be replaced!
- ManagedImportRequest.buildResponse() (N times, outside the transaction)
- Only step 4 does anything, storing the pixels in a ImportResponse
- ManagedImportRequest.getResponse() (1 time, regardless of exception or
not)
- Performs cleanup, then returns the ImportResponse assuming that no
call to helper.cancel() has been made. At this point,
ImportLibrary.importImage() returns successfully.