Blitz Gateway documentation

This page provides some background information on the OMERO Python client ‘gateway’ (omero.gateway module).

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, to provide connection and data retrieval services to various web clients. However, we encourage its use for all access to the OMERO Python API.

Connection wrapper

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 retrieving data objects from OMERO.

Model object wrappers

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.

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 ProjectI
from omero.rtypes import rstring
p = 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 ProjectWrapper
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).

>>> from omero.gateway import BlitzGateway

>>> conn = BlitzGateway("username", "password", host="localhost", port=4064)
>>> conn.connect()

>>> 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
>>> conn.close()

Unicode

When unwrapping omero.rtypes.rstring attributes from omero.model.object instances as shown above, the BlitzObjectWrapper subclasses will decode the utf8-encoded string and return the resulting unicode string.

However, some methods added to BlitzObjectWrappers will return regular strings as follows:

BlitzObjectWrapper.getName()            except ExperimenterWrapper.getName() and LogicalChannelWrapper.getName()
BlitzObjectWrapper.getDescription()
AnnotationWrapper.getNs()
FileAnnotationWrapper.getFileName()
TagAnnotationWrapper.getValue()
CommentAnnotationWrapper.getValue()
MapAnnotationWrapper.getValue()  - list of strings
PlateWrapper.getColumnLabels() / getRowLabels()   - list of strings or integers
WellWrapper.getWellPos()
ColorHolder.getHtml() / getCss()
ChannelWrapper.getLut()
ImageWrapper.getChannelLabels()  - list of strings

When using unicode strings, care must be taken when printing to the console if they include non-ASCII characters as described here.

When using the BlitzGateway in the OMERO.web framework, Django will convert strings into unicode strings so it is safe to use either. See Django Unicode data.

Wrapper coverage

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.

Access to the OMERO API services

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 getXXX methods e.g. getQueryService) are always reused for each call, e.g. conn.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()

Stateful services, reconnection, error handling etc.

The Blitz gateway was designed for use in the OMERO.web framework and it is not expected that stateful services will be maintained on the client for significant time. There are various error-handling functionalities 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. Our general advice is to create, use and close the stateful services in the shortest practicable time.

try:
    image = conn.getObject("Image", image_id)
    # Initializes the Rendering engine and sets rendering settings
    image.setActiveChannels([1, 2], [[20, 300], [50, 500]], ['00FF00', 'FF0000'])
    pil_image = image.renderImage(0, 0)
    # Now we close the rendering engine
    image._re.close

# Can continue to use the connection until done,
# then close ALL services:
finally:
    conn.close()

Overwriting and extending omero.gateway classes

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. N.B. The call to omero.gateway.refreshWrappers() is important to update the dictionary of classes used by conn.getObjects(). This will ensure that instances of your class are returned by conn.getObjects().

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()