Note
This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected before the end of 2016.
The Sphinx-generated documentation of methods provided by OMERO Gateway is available showing wrapper classes.
Specifically, the API for the ‘conn’ connection wrapper created above is here.
When working with OMERO model objects (omero.model.Image etc) the Gateway will wrap these objects in classes such as omero.gateway.ImageWrapper to handle object loading and hierarchy traversal. For example:
>>> for p in conn.listProjects(): # Initially we just load Projects
... print p.getName()
... for dataset in p.listChildren(): # lazy-loading of Datasets here
... print " ", dataset.getName()
...
TestProject
Aurora-B
tiff stacks
newTimeStack
test
siRNAi
CENP
live-cell
survivin
If you need access to API methods that are not provided by the gateway library, you can get hold of the OMERO Application Programming Interface.
Note
These services will always work with omero.model objects and not the gateway wrapper objects.
The gateway handles creation and reuse of the API services, so that new ones are not created unnecessarily. Services can be accessed using the methods of the underlying Service Factory with the Gateway handling reuse as needed. Stateless services (those retrieved with get… methods e.g. getQueryService) are always reused for each call, e.g. blitzon.getQueryService() whereas stateful services e.g. createRenderingEngine may be created each time.
Not all methods of the service factory are currently supported in the gateway. You can get an idea of the currently supported services by looking at the source code under the _createProxies method.
Example: ContainerService can load Projects and Datasets in a single call to server (no lazy loading)
cs = conn.getContainerService()
projects = cs.loadContainerHierarchy("Project", None, None)
for p in projects: # omero.model.ProjectI
print p.getName().getValue() # need to 'unwrap' rstring
for d in p.linkedDatasetList():
print d.getName().getValue()
The Blitz gateway was designed for use in the OMERO.web framework framework and it is not expected that stateful services will be maintained on the client for significant time. There is various error-handling functionality in the Blitz gateway that will close existing services and recreate them in order to maintain a working connection. If this happens then any stateful services that you have on the client-side will become stale. We will attempt to document this a little better in due course, but our general advice is to create, use and close the stateful services in the shortest practicable time.
When working with omero.gateway or wrapper classes such as omero.gateway.ImageWrapper you might want to add your own functionality or customize an existing one. NB: Note the call to omero.gateway.refreshWrappers() to ensure that your subclasses are returned by calls to getObjects() For example:
class MyBlitzGateway (omero.gateway.BlitzGateway):
def __init__ (self, *args, **kwargs):
super(MyBlitzGateway, self).__init__(*args, **kwargs)
...do something, e.g. add new field...
self.new_field = 'foo'
def connect (self, *args, **kwargs):
rv = super(MyBlitzGateway, self).connect(*args,**kwargs)
if rv:
...do something, e.g. modify new field...
self.new_field = 'bla'
return rv
omero.gateway.BlitzGateway = MyBlitzGateway
class MyBlitzObjectWrapper (object):
annotation_counter = None
def countAnnotations (self):
"""
Count on annotations linked to the object and set the value
on the custom field 'annotation_counter'.
@return Counter
"""
if self.annotation_counter is not None:
return self.annotation_counter
else:
container = self._conn.getContainerService()
m = container.getCollectionCount(self._obj.__class__.__name__, type(self._obj).ANNOTATIONLINKS, [self._oid], None)
if m[self._oid] > 0:
self.annotation_counter = m[self._oid]
return self.annotation_counter
else:
return None
class ImageWrapper (MyBlitzObjectWrapper, omero.gateway.ImageWrapper):
"""
omero_model_ImageI class wrapper overwrite omero.gateway.ImageWrapper
and extends MyBlitzObjectWrapper.
"""
def __prepare__ (self, **kwargs):
if kwargs.has_key('annotation_counter'):
self.annotation_counter = kwargs['annotation_counter']
omero.gateway.ImageWrapper = ImageWrapper
# IMPORTANT to update the map of wrappers for 'Image' etc. returned by getObjects("Image")
omero.gateway.refreshWrappers()
This page provides some background information on the OMERO Python client ‘gateway’ (omero.gateway module) and describes work to improve the API.
The Blitz Gateway is a Python client-side library that facilitates working with the OMERO API, handling connection to the server, loading of data objects and providing convenience methods to access the data. It was originally designed as part of the OMERO.web framework framework, to provide connection and data retrieval services to various web clients. However, we have now decided to encourage its use for all access to the OMERO Python API.
The Gateway consists of a number of wrapper objects:
The BlitzGateway class (see API of development code) is a wrapper for the OMERO client and session objects. It provides various methods for connecting to the OMERO server, querying the status or context of the current connection and as a starting point for retrieving data objects from OMERO.
from omero.gateway import *
conn = BlitzGateway("username", "password", host="localhost", port=4064)
conn.connect()
for p in conn.listProjects():
print p.name
OMERO model objects, e.g. omero.model.Project, omero.model.Pixels etc. (see full list) are code-generated and mapped to the OMERO database schema. They are language agnostic and their data is in the form of omero.rtypes as described in about model objects).
import omero
from omero.model import *
from omero.rtypes import rstring
p = omero.model.ProjectI()
p.name = rstring("My Project") # attributes are all rtypes
print p.getName().getValue() # getValue() to unwrap the rtype
print p.name.val # short-hand
To facilitate work in Python, particularly in web page templates, these Python model objects are wrapped in Blitz Object Wrappers. This hides the use of rtypes.
import omero
from omero.model import *
from omero.rtypes import rstring
p = omero.model.ProjectI()
p.setName(rstring("Omero Model Project")) # attributes are all rtypes
print p.getName().getValue() # getValue() to unwrap the rtype
print p.name.val # short-hand
from omero.gateway import *
project = ProjectWrapper(obj=p) # wrap the model.object
project.setName("Project Wrapper") # Don't need to use rtypes
print project.getName()
print project.name
print project._obj # access the wrapped object with ._obj
These wrappers also have a reference to the BlitzGateway connection wrapper, so they can make calls to the server and load more data when needed (lazy loading).
E.g.
# connect as above
for p in conn.listProjects():
print p.name
for dataset in p.listChildren(): # lazy loading of datasets, wrapped in DatasetWrapper
print "Dataset", d.name
The OMERO data model has a large number of objects, not all of which are used by the OMERO.web framework. Therefore, the Blitz gateway (which was originally built for this framework) has not yet been extended to wrap every omero.model object with a specific Blitz Object Wrapper. The current list of object wrappers can be found in the omero.gateway module API. As more functionality is provided by the Blitz Gateway, the coverage of object wrappers will increase accordingly.