The omero::api module defines all the central verbs for working with OMERO.blitz.
Arguments and return values consist of those
types defined in the other ice files available here. With no further custom code, it is possible to interoperate with OMERO.blitz simply via the definitions here. Start with the ServiceFactory definition at the end of this file.
Note: Using these types is significantly easier in combination with
the JavaDocs of the OMERO.server, specifically the ome.api package. Where not further noted below, the follow mappings between ome.api argument types and omero::api argument types hold:
| ome.api | omero::api |
| java.lang.Class | string |
| java.util.Set | java.util.List/vector |
| IPojo options (Map) | omero::sys::ParamMap |
| If null needed | omero::RType subclass |
| ... | ... |
Bases: Ice.Object
Primary callback interface for interaction between client and server session (“ServiceFactory”). Where possible these methods will be called one-way to prevent clients from hanging the server.
Heartbeat-request made by the server to guarantee that the client is alive. If the client is still active, then some method should be made on the server to update the last idle time.
The session to which this ServiceFactory is connected has been closed. Almost no further method calls (if any) are possible. Create a new session via omero.client.createSession()
Message that the server will be shutting down in the given number of milliseconds, after which all new and running method invocations will recieve a CancelledException.
Bases: IcePy.ObjectPrx
Heartbeat-request made by the server to guarantee that the client is alive. If the client is still active, then some method should be made on the server to update the last idle time.
Bases: omero.api.StatefulServiceInterface
Stateful service for generating OME-XML or OME-TIFF from data stored in OMERO. Intended usage:
ExporterPrx e = sf.createExporter();
// Exporter is currently in the “configuration” state // Objects can be added by id which should be present // in the output.
e.addImage(1);
// As soon as a generate method is called, the objects // added to the Exporter are converted to the specified // format. The length of the file produced is returned. // No more objects can be added to the Exporter, nor can // another generate method be called.
long length = e.generateTiff();
// As soon as the server-side file is generated, read() // can be called to get file segments. To create another // file, create a second Exporter. Be sure to close all // Exporter instances.
long read = 0 byte[] buf; while (true) { buf = e.read(read, 1000000); // Store to file locally here if (buf.length
Adds a single image with basic metadata to the Exporter for inclusion on the next call to getBytes().
Generates an OME-TIFF file. The return value is the length of the file produced. This method ends configuration.
Generates an OME-XML file. The return value is the length of the file produced.
Returns “length” bytes from the output file. The file can be safely read until reset() is called.
Bases: omero.api.StatefulServiceInterfacePrx
Adds a single image with basic metadata to the Exporter for inclusion on the next call to getBytes().
Bases: omero.api.ServiceInterface
See IAdmin.html
HasPassword: Requires the session to have been created with a password as opposed to with a session uuid (via joinSession). If that’s not the case, a SecurityViolation will be thrown, in which case ServiceFactory.setSecurityPassword can be used.
HasPassword: Requires the session to have been created with a password as opposed to with a session uuid (via joinSession). If that’s not the case, a SecurityViolation will be thrown, in which case ServiceFactory.setSecurityPassword can be used.
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IConfig.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IContainer.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See ILdap.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IMetadata.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IPixels.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IProjection.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IQuery.html
Return a sequence of omero.RType sequences.
Each element of the outer sequence is one row in the return value. Each element of the inner sequence is one column specified in the HQL.
omero.model.IObject instances are returned wrapped in an omero.rtype.RObject instance. Primitives are mapped to the expected omero.RType subclass. Types without an omero.RType mapper if returned will throw an exception if present in the select except where a manual conversion is present on the server. This includes:
omero.model.Permissions instances are serialized to an omero.RMap containing the keys: perms, canAnnotate, canEdit, canLink, canDelete
The quantity types like omero.model.Length are serialized to an omero.RMap containing the keys: value, unit, symbol
As with SQL, if an aggregation statement is used, a group by clause must be added.
Examples:
select i.name, i.description from Image i where i.name like ‘%.dv’
select tag.textValue, tagset.textValue from TagAnnotation tag join tag.annotationLinks l join l.child tagset
select p.pixelsType.value, count(p.id) from Pixel p group by p.pixelsType.value
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IRenderingSettings.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IRepositoryInfo.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
Interface for working with regions of interest.
Returns all the Rois in an Image, indexed via Shape.
Loads Rois as findByRoi.
Returns all the Rois on the given plane, indexed via Shape.
Loads Rois as findByRoi.
Returns a RoiResult with a single Roi member. Shape linkages are properly created. All Shapes are loaded, as is the Pixels and Image object. TODO: Annotations?
Returns a map from omero.model.FileAnnotation ids to RoiResult instances. Logic is identical to getMeasuredRois, but Roi data will not be duplicated. (i.e. the objects are referentially identical)
Loads the ROIs which are linked to by the given omero.model.FileAnnotation id for the given image.
Calculate the points contained within a given shape
Returns a list of omero.model.FileAnnotation instances with the namespace “openmicroscopy.org/measurements” which are attached to the omero.model.Plate containing the given image AND which are attached to at least one omero.model.Roi
ownership of the annotation.
Calculate stats for all the shapes within the given Roi.
Calculate the stats for the points within the given Shapes.
Calculate the stats for the points within the given Shape.
Returns the OMERO.tables service via the omero.model.FileAnnotation id returned by getImageMeasurements.
Bases: omero.api.ServiceInterfacePrx
Returns a RoiResult with a single Roi member. Shape linkages are properly created. All Shapes are loaded, as is the Pixels and Image object. TODO: Annotations?
Bases: omero.api.ServiceInterface
Utility service for managing and launching scripts for execution by the Processor API.
Typical usage might include (PYTHON):
sf = client.createSession() svc = sf.getScriptService() scripts = svc.getScripts()
if len(scripts) >= 1: script_id = svc.keys()[-1] else: script_id = svc.uploadScript(‘/test/my_script.py’, SCRIPT_TEXT)
params = svc.getParams(script_id)
# You will need to parse the params to create the proper input inputs = {}
# The last parameter is how long to wait as an RInt proc = svc.runScript(script_id, inputs, None) try: cb = omero.scripts.ProcessCallbackI(client, proc) while not cb.block(1000): # ms. pass cb.close() rv = proc.getResults(0) finally: proc.close(False)
See OMERO.scripts for more information.
Returns true if there is a processor which will run the given script.
Either the script is an official script and this method will return true (though an individual invocation may fail with an omero.ResourceError for some reason) or this is a user script, and a usermode processor must be active which takes the scripts user or group.
Delete the script on the server with id. The file will also be removed from disk.
Modify the text for the given script object.
Get the parameters that the script takes and returns, along with other metadata available from the script.
Get the id of an official script by the script path. The script service ensures that all script paths are unique.
Note: there is no similar method for user scripts (e.g. getUserScriptID) since the path is not guaranteed to be unique.
Get the text from the server for the script with given id.
Get the script from the server with details from OriginalFile Arguments:
scriptID see above
This method returns official server scripts as a list of omero.model.OriginalFile objects. These scripts will be executed by the server if submitted via runScript. The input parameters necessary for proper functioning can be retrieved via getParams.
The omero.model.OriginalFile#path value can be used in other official scripts via the language specific import command, since the script directory will be placed on the appropriate environment path variable.
scripts = scriptService.getScripts() for script in scripts: text = scriptService.getScriptText(script.id.val) path = script.path.val[1:] # First symbol is a “/” path = path.replace(“/”,”.”) print “Possible import: %s” % path
Returns non-official scripts which have been uploaded by individual users. These scripts will not be run by the server, though a user can start a personal “usermode processor” which will allow the scripts to be executed. This is particularly useful for testing new scripts.
If ResourceError is thrown, then no Processor is available. Use scheduleJob to create a omero.model.ScriptJob in the “Waiting” state. A Processor may become available.
try: proc = scriptService.runScript(1, {}, None) except ResourceError: job = scriptService.scheduleScript(1, {}, None)
The ScriptProcess proxy MUST be closed before exiting. If you would like the script execution to continue in the background, pass “True” as the argument.
try: proc.poll() # See if process is finished finally: proc.close(True) # Detach and execution can continue # proc.close(False) # OR script is immediately stopped.
Like uploadScript but is only callable by administrators. The parameters for the script are also checked.
Upload a user script to the server and return the id. This method checks that a script with that names does not exist and that the script has parameters if possible, i.e. a usermode processor is running which for the current user.
Used internally by processor.py to check if the script attached to the omero.model.Job has a valid script attached, based on the acceptsList and the current security context.
An example of an acceptsList might be Experimenter(myUserId, False), meaning that only scripts belonging to me should be trusted. An empty list implies that the server should return what it would by default trust.
A valid script will be returned if it exists; otherwise null.
Bases: omero.api.ServiceInterfacePrx
This method returns official server scripts as a list of omero.model.OriginalFile objects. These scripts will be executed by the server if submitted via runScript. The input parameters necessary for proper functioning can be retrieved via getParams.
The omero.model.OriginalFile#path value can be used in other official scripts via the language specific import command, since the script directory will be placed on the appropriate environment path variable.
scripts = scriptService.getScripts() for script in scripts: text = scriptService.getScriptText(script.id.val) path = script.path.val[1:] # First symbol is a “/” path = path.replace(“/”,”.”) print “Possible import: %s” % path
Bases: omero.api.ServiceInterface
See ISession.html
HasPassword: Requires the session to have been created with a password as opposed to with a session uuid (via joinSession). If that’s not the case, a SecurityViolation will be thrown, in which case ServiceFactory.setSecurityPassword can be used.
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IShare.html
Bases: omero.api.ServiceInterface
Service for the querying of OMERO metadata based on creation and modification time. Currently supported types for querying include:
The map return values will be indexed by the short type name above: “Project”, “Image”, ... All keys which are passed in the StringSet argument will be included in the returned map, even if they have no values. A default value of 0 or the empty list [] will be used. The only exception to this rule is that the null or empty StringSet implies all valid keys.
All methods take a omero::sys::Parameters object and will apply the filter object for paging through the data in order to prevent loading too many objects. If the parameters argument is null or no paging is activated, then the default will be: OFFSET=0, LIMIT=50. Filter.ownerId and Filter.groupId will also be AND’ed to the query if either value is present. If both are null, then the current user id will be used. To retrieve for all users, use ownerId == rlong(-1) and groupId == null.
The methods which take a StringSet and a Parameters object, also have a “bool merge” argument. This argument defines whether or not the LIMIT applies to each object independently ([“a”,”b”] @ 100 == 200) or merges the lists together chronologically ([“a”,”b”] @ 100 merged == 100).
Except for Image, IObject.details.updateEvent is used in all cases for determining most recent events. Images are compared via Image.acquisitionDate which is unlike the other properties is modifiable by the user.
A typical invocation might look like (in Python):
timeline = sf.getTimelineService() params = ParametersI().page(0,100) types = [“Project”,”Dataset”]) map = timeline.getByPeriod(types, params, False)
At this point, map will not contain more than 200 objects.
This service is defined only in Blitz and so no javadoc is available in the ome.api package.
TODOS: binning, stateful caching, ...
Queries the same information as getByPeriod, but only returns the counts for the given objects.
Returns the given LIMIT objects of TYPES as ordered by creation/modification times in the Event table, but within the given time window.
Returns the EventLog table objects which are queried to produce the counts above. Note the concept of “period inclusion” mentioned above.
WORKAROUND WARNING: this method returns non-managed EventLogs (i.e. eventLog.getId() == null) for “Image acquisitions”.
Return the last LIMIT annotation __Links__ whose parent (IAnnotated) matches one of the parentTypes, whose child (Annotation) matches one of the childTypes (limit of one for the moment), and who namespace matches via ILIKE.
The parents and children will be unloaded. The link will have its creation/update events loaded.
If Parameters.theFilter.ownerId or groupId are set, they will be AND’ed to the query to filter results.
Merges by default based on parentType.
Returns the last LIMIT objects of TYPES as ordered by creation/modification times in the Event table.
Return the last LIMIT comment annotation links attached to a share by __others__.
Note: Currently the storage of these objects is not optimal and so this method may change.
Bases: omero.api.ServiceInterfacePrx
Return the last LIMIT annotation __Links__ whose parent (IAnnotated) matches one of the parentTypes, whose child (Annotation) matches one of the childTypes (limit of one for the moment), and who namespace matches via ILIKE.
The parents and children will be unloaded. The link will have its creation/update events loaded.
If Parameters.theFilter.ownerId or groupId are set, they will be AND’ed to the query to filter results.
Merges by default based on parentType.
Bases: omero.api.ServiceInterface
See ITypes.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.ServiceInterface
See IUpdate.html
Bases: omero.api.ServiceInterfacePrx
Bases: omero.api.StatefulServiceInterface
See JobHandle.html
Bases: omero.api.StatefulServiceInterfacePrx
Bases: omero.api.StatefulServiceInterface
Server-side interface for import.
Bases: omero.api.StatefulServiceInterfacePrx
Bases: omero.api.StatefulServiceInterface
Retrieves a more complete definition of the resolution level in question. The size of this array will be of length getResolutionLevels.
Retrieves the active resolution level. Returns:
The active resolution level.
Retrieves the number of resolution levels that the backing pixels pyramid contains. Returns:
The number of resolution levels. This value does not
necessarily indicate either the presence or absence of a pixels pyramid.
Retrieves the tile size for the pixel store. Returns:
An array of length = 2 where the first
value of the array is the tile width and the second value is the tile height.
Whether or not this raw pixels store requires a backing pixels pyramid to provide sub-resolutions of the data. Returns:
true if the pixels store requires a
pixels pyramid and false otherwise.
Sets the active resolution level. Arguments:
resolutionLevel The resolution level to be used by
the pixel buffer.
Bases: omero.api.StatefulServiceInterfacePrx
Whether or not this raw pixels store requires a backing pixels pyramid to provide sub-resolutions of the data. Returns:
true if the pixels store requires a
pixels pyramid and false otherwise.
Bases: omero.api.StatefulServiceInterface
Raw file gateway which provides access to the OMERO file repository.
Note: methods on this service are protected by a “DOWNLOAD” restriction.
See also RawFileStore.html
Returns the current file id or null if none has been set.
This method manages the state of the service. This method will throw a omero.SecurityViolation if for the current user context either the file is not readable or a omero.constants.permissions#DOWNLOAD restriction is in place.
Bases: omero.api.StatefulServiceInterfacePrx
This method manages the state of the service. This method will throw a omero.SecurityViolation if for the current user context either the file is not readable or a omero.constants.permissions#DOWNLOAD restriction is in place.
Bases: omero.api.PyramidService
Binary data provider. Initialized with the ID of a omero.model.Pixels instance, this service can provide various slices, stacks, regions of the 5-dimensional (X-Y planes with multiple Z-sections and Channels over Time). The byte array returned by the getter methods and passed to the setter methods can and will be interpreted according to results of getByteWidth(), isFloat(), and isSigned().
Read-only caveat:
Mutating methods (set*) are only available during the first access. Once the Pixels data has been successfully saved (via the save or close methods on this interface), then the data should be treated read-only. If Pixels data writing fails and the service is inadvertently closed, delete the Pixels object, and create a new one. Any partially written data will be removed.
Calculates a SHA-1 message digest for the entire pixel store. Returns:
byte array containing the message digest.
Returns the byte width for the pixel store. Returns:
See above.
Retrieves a particular column from this pixel store. Arguments:
x offset across the X-axis of the pixel store. z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
Retrieves a n-dimensional block from this pixel store. Arguments:
start offset for each dimension within pixel store. size of each dimension (dependent on dimension). step needed of each dimension (dependent on dimension).
Returns the current Pixels set identifier. Returns:
See above.
Returns the current Pixels path. Returns:
See above.
Retrieves the offset for a particular 2D image plane in this pixel store. Arguments:
z offset across the Z-axis of the pixel buffer. c offset across the C-axis of the pixel buffer. t offset across the T-axis of the pixel buffer.
Retrieves a region from a given plane from this pixel store. Arguments:
z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store. count the number of pixels to retrieve. offset the offset at which to retrieve count pixels.
given 2D image plane. It is guaranteed that this buffer will have been byte swapped.
Retrieves the in memory size of a 2D image plane in this pixel store. Returns:
2D image plane size in bytes (sizeX*sizeY*ByteWidth).
Retrieves a particular 2D image plane from this pixel store. Arguments:
z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
Retrieves a region from this pixel store. Arguments:
size byte width of the region to retrieve. offset offset within the pixel store.
Retrieves the offset for a particular row or scanline in this pixel store. Arguments:
y offset across the Y-axis of the pixel buffer. z offset across the Z-axis of the pixel buffer. c offset across the C-axis of the pixel buffer. t offset across the T-axis of the pixel buffer.
Retrieves the in memory size of a row or scanline of pixels in this pixel store. Returns:
row or scanline size in bytes (sizeX*ByteWidth)
Retrieves a particular row or scanline from this pixel store. Arguments:
y offset across the Y-axis of the pixel store. z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store. Arguments:
c offset across the C-axis of the pixel buffer. t offset across the T-axis of the pixel buffer.
Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store. Returns:
stack size in bytes (sizeX*sizeY*sizeZ*ByteWidth).
Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store. Arguments:
c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
Retrieves a tile from this pixel buffer. Arguments:
z offset across the Z-axis of the pixel buffer. c offset across the C-axis of the pixel buffer. t offset across the T-axis of the pixel buffer. x Top left corner of the tile, X offset. y Top left corner of the tile, Y offset. w Width of the tile. h Height of the tile.
Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store. Arguments:
t offset across the T-axis of the pixel buffer.
Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store. Returns:
timepoint size in bytes (sizeX*sizeY*sizeZ*sizeC*ByteWidth).
Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store. Arguments:
t offset across the T-axis of the pixel store.
Retrieves the in memory size of the entire pixel store. Returns:
total size of the pixel size in bytes
(sizeX*sizeY*sizeZ*sizeC*sizeT*ByteWidth).
Returns whether or not the pixel buffer has floating point pixels. Returns:
Returns whether or not the pixel store has signed pixels. Returns:
See above.
Prepares the stateful service with a cache of loaded Pixels objects. This method is designed to combat query overhead, where many sets of Pixels are to be read from or written to, by loading all the Pixels sets at once. Multiple calls will result in the existing cache being overwritten. Arguments:
pixelsIds Pixels IDs to cache.
Save the current state of the pixels, updating the SHA1. This should only be called AFTER all data is successfully set. Future invocations of set methods may be disallowed. This read-only status will allow background processing (generation of thumbnails, compression, etc) to begin. More information under RawPixelsStore.
A null instance will be returned if no save was performed.
Initializes the stateful service for a given Pixels set. Arguments:
pixelsId Pixels set identifier. bypassOriginalFile Whether or not to bypass checking for an
original file to back the pixel buffer used by this service. If requests are predominantly write-only or involve the population of a brand new pixel buffer using true here is a safe optimization otherwise false is expected.
See “read-only caveat” under RawPixelsStore
Sets a particular 2D image plane in this pixel store. Arguments:
buf a byte array of the data comprising this 2D image plane. z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
See “read-only caveat” under RawPixelsStore
Sets a region in this pixel buffer. Arguments:
size byte width of the region to set. offset offset within the pixel buffer. buf a byte array of the data.
See “read-only caveat” under RawPixelsStore
Sets a particular row or scanline in this pixel store. Arguments:
buf a byte array of the data comprising this row or scanline. y offset across the Y-axis of the pixel store. z offset across the Z-axis of the pixel store. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
See “read-only caveat” under RawPixelsStore
Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store. Arguments:
buf a byte array of the data comprising this stack. c offset across the C-axis of the pixel store. t offset across the T-axis of the pixel store.
See “read-only caveat” under RawPixelsStore
Sets a tile in this pixel buffer. Arguments:
buf A byte array of the data. z offset across the Z-axis of the pixel buffer. c offset across the C-axis of the pixel buffer. t offset across the T-axis of the pixel buffer. x Top left corner of the tile, X offset. y Top left corner of the tile, Y offset. w Width of the tile. h Height of the tile.
end of the file.
See “read-only caveat” under RawPixelsStore
Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store. Arguments:
buf a byte array of the data comprising this timepoint. t offset across the T-axis of the pixel buffer.
See “read-only caveat” under RawPixelsStore
Bases: omero.api.PyramidServicePrx
Initializes the stateful service for a given Pixels set. Arguments:
pixelsId Pixels set identifier. bypassOriginalFile Whether or not to bypass checking for an
original file to back the pixel buffer used by this service. If requests are predominantly write-only or involve the population of a brand new pixel buffer using true here is a safe optimization otherwise false is expected.
See “read-only caveat” under RawPixelsStore
Bases: omero.api.PyramidService
See RenderingEngine.html
Bases: omero.api.PyramidServicePrx
Bases: Ice.Object
Bases: IcePy.ObjectPrx
Bases: Ice.Object
Specifies filters used when querying the ROIs.
Bases: IcePy.ObjectPrx
Bases: Ice.Object
Returned by most search methods. The RoiOptions is the options object passed into a method, possibly modified by the server if some value was out of range. The RoiList contains all the Rois which matched the given query.
The individual shapes of the Rois which matched can be found in the indexes. For example, all the shapes on z=1 can by found by:
ShapeList shapes = byZ.get(1);
Shapes which are found on all z, t, or do not belong to a group can be found with:
byZ.get(-1); byT.get(-1); byG.get(“”);
respectively. The groups string-string map provides the hierarchy of the group strings using unix-style filesystem paths. That is, if a returned shape is in the group “/a/b”, then there will be an entry in the groups map: ...TBD...
Bases: IcePy.ObjectPrx
Bases: Ice.Object
Container for ShapeStats, one with the combined values, and one per shape.
Bases: IcePy.ObjectPrx
Bases: omero.cmd.Request
Bases: omero.cmd.RequestPrx
Bases: omero.cmd.Response
Bases: omero.cmd.ResponsePrx
Bases: omero.api.StatefulServiceInterface
See Search.html
Bases: omero.api.StatefulServiceInterfacePrx
Bases: omero.cmd.Session
Starting point for all OMERO.blitz interaction.
A ServiceFactory once acquired can be used to create any number
of service proxies to the server. Most services implement ServiceInterface or its subinterface StatefulServiceInterface.
Returns a list of string ids for currently active services. This will _not_ keep services alive, and in fact checks for all expired services and removes them.
Marks the session for closure rather than detachment, which will be triggered by the destruction of the Glacier2 connection via router.destroySession()
Closing the session rather the detaching is more secure, since all resources are removed from the server and can safely be set once it is clear that a client is finished with those resources.
Allows looking up any stateful service by name.
See Constants.ice for examples of services. If a service has been added by third-parties, createByName can be used even though no concrete method is available.
Marks the session for detachment rather than closure, which will be triggered by the destruction of the Glacier2 connection via router.destroySession()
This is the default and allows a lost session to be reconnected, at a slight security cost since the session will persist longer and can be used by others if the UUID is intercepted.
Allows looking up any stateless service by name.
See Constants.ice for examples of services. If a service has been added by third-parties, getByName can be used even though no concrete method is available.
Provides a list of all valid security contexts for this session. Each of the returned omero.model.IObject instances can be passed to setSecurityContext.
Returns true if the given service is alive.
Except for fatal server or session errors, this method should never throw an exception.
Requests that the given services be marked as alive. It is possible that one of the services has already timed out, in which case the returned long value will be non-zero.
Specifically, the bit representing the 0-based index will be 1:
if (retval & 1<<idx == 1<<idx) { // not alive }
Except for fatal server or session errors, this method should never throw an exception.
Sets the single callback used by the ServiceFactory to communicate with the client application. A default callback is set by the omero::client object on session creation which should suffice for most usage.
See the client object’s documentation in each language mapping for ways to use the callback.
Changes the security context for the current session.
A security context limits the set of objects which will
be returned by all queries and restricts what updates can be made.
Current valid values for security context:
omero.model.ExperimenterGroup - logs into a specific group omero.model.Share - uses IShare to activate a share
Passing an unloaded version of either object type will change
the way the current session operates. Note: only objects which are returned by the getSecurityContexts method are considered valid. Any other instance will cause an exception to be thrown.
Example usage in Python:
sf = client.createSession() objs = sf.getSecurityContexts() old = sf.setSecurityContext(objs[-1])
Re-validates the password for the current session. This prevents
See methods that mention “HasPassword”.
Returns a reference to a back-end manager. The omero.grid.SharedResources service provides look ups for various facilities offered by OMERO:
OMERO.scripts OMERO.tables
These facilities may or may not be available on first request.
Subscribe to a given topic. The topic must exist and the user must have sufficient permissions for that topic. Further the proxy object must match the required type for the topic as encoded in the topic name.
Bases: omero.cmd.SessionPrx
Provides a list of all valid security contexts for this session. Each of the returned omero.model.IObject instances can be passed to setSecurityContext.
Bases: Ice.Object
Service marker similar to ome.api.ServiceInterface. Any object which IS-A ServiceInterface but IS-NOT-A StatefulServiceInterface (below) is be definition a “stateless service”
Bases: IcePy.ObjectPrx
Bases: Ice.Object
Contains a discrete representation of the geometry of an omero::model::Shape. The x and y array are of the same size with each pair of entries representing a single point in the 2D plane.
Bases: IcePy.ObjectPrx
Bases: Ice.Object
Contains arrays, one entry per channel, of the statistics for a given shape. All arrays are the same size, except for the channelIds array, which specifies the ids of the logical channels which compose this Shape. If the user specified no logical channels for the Shape, then all logical channels from the Pixels will be in channelIds.
Bases: IcePy.ObjectPrx
Bases: omero.api.ServiceInterface
Service marker for stateful services which permits the closing of a particular service before the destruction of the session.
Load a service implementation from disk if it was previously passivated. It is unnecessary to call this method since activation happens automatically, but calling this may prevent a short lapse when the service is first accessed after passivation.
It is safe to call this method at any time, even when the service is not passivated.
Frees all resources – passivated or active – for the given stateful service and removes its name from the object adapter. Any further method calls will fail with a Ice::NoSuchObjectException.
Note: with JavaEE, the close method was called publically, and internally this called destroy(). As of the OmeroBlitz migration, this functionality has been combined.
To free clients from tracking the mapping from session to stateful service, each stateful service can returns its own context information.
Causes the blitz server to store the service implementation to disk to free memory. This is typically done automatically by the server when a pre-defined memory limit is reached, but can be used by the client if it clear that a stateful service will not be used for some time.
Activation will happen automatically whether passivation was done manually or automatically.
Bases: omero.api.ServiceInterfacePrx
Causes the blitz server to store the service implementation to disk to free memory. This is typically done automatically by the server when a pre-defined memory limit is reached, but can be used by the client if it clear that a stateful service will not be used for some time.
Activation will happen automatically whether passivation was done manually or automatically.
Bases: omero.api.StatefulServiceInterface
See ThumbnailStore.html
Bases: omero.api.StatefulServiceInterfacePrx
