[ome-users] matlab accessing shared data

[Alexander Tournier]

Thanks Josh and Jmarie,

I've looked at the doc you sent me and am now trying to move away from 
using the gateway service and use the ContainerService instead.

I've been playing with the demo matlab scripts and I get a weird error 
after:
projectsList = proxy.loadContainerHierarchy(omero.model.Project.class, 
[], param);
The error message is:
The class omero.model.Project has no property or method named 'class'.

The omero class is loaded correctly so I'm at a loss here.
I am using the current 4.3.3 release

Minimal script:
addpath('/farm/home/tourni01/Projects/2-ImageAnalysis/13-OME/OMERO.matlab-4.3.3')
OmeroClient_Jar = fullfile(findOmero, 'omero_client.jar');
javaaddpath(OmeroClient_Jar);
import omero.*;

ice_config = fullfile(findOmero, 'ice.config');
args = javaArray('java.lang.String',1);
args(1) = java.lang.String(['--Ice.Config=',ice_config]);
client = omero.client(args);
session = client.createSession();
t = omeroKeepAlive(client);

userId = session.getAdminService().getEventContext().userId
groupId = session.getAdminService().getEventContext().groupId

proxy = session.getContainerService();

param = omero.sys.ParametersI();
param.noLeaves();%indicate not to load the images
param.exp(omero.rtypes.rlong(userId));

projectsList = proxy.loadContainerHierarchy(omero.model.Project.class, 
[], param);

Any ideas??
Thanks,
Alex



On 20/01/12 20:03, Josh Moore wrote:
>
>
> On Jan 19, 2012, at 4:51 PM, Josh Moore wrote:
>
>> Forwarding to the list.
>>
>> On Jan 19, 2012, at 4:49 PM, Alexander Tournier wrote:
>>
>>> Hi Josh,
> Hi Alex,
>
>>> thanks for your answer.
>>> I'm still stuck.
>>> I'm using getProjects from the createGateway service, this lists all my projects (in the collaborative group) but not my collaborators.
> In 4.4, we will be suggesting every move away from use of GatewayPrx.
>
>>> I've been looking into
>>> http://trac.openmicroscopy.org.uk/ome/wiki/OmeroApi
> Instead, take a look at http://hudson.openmicroscopy.org.uk/job/OMERO/javadoc/ome/api/IContainer.html
>
> Examples of its use are available under:
>
>     https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/java/src/training/ReadData.java
>
> Hope that helps.
> Cheers,
> ~Josh
>
>>> To find out about it's limitations but can't find any documentation on it.
>>> Am I looking in the best place for this??
>>>
>>> Thanks
>>> Alex
>>>
>>>
>>>
>>>
>>> On 16/01/12 08:28, Josh Moore wrote:
>>>> On Jan 13, 2012, at 3:17 PM, Alexander Tournier wrote:
>>>>
>>>>> Hi there,
>>>> Hi Alexander,
>>>>
>>>>> I'm using matlab to access/analyse and store processed images.
>>>>> I can now access my own data but can't access the data shared in the same (which I can access in OMERO.insight).
>>>>>
>>>>> - is there a way to specify in matlab which group one wants to access (currently have to go into OMERO.Insight and change it there, this seems to carry across to what matlab can see)
>>>> There are several options.
>>>>
>>>> * In your ice.config file you can set omero.group to the group id that you want to be logged into.
>>>>
>>>> * You can pass omero.group in to loadOmero:
>>>>
>>>>>> p = java.util.Properties();
>>>>>> p.setProperty('omero.group','your-group');
>>>>>> p.setProperty('omero.host','localhost');
>>>>>> p.setProperty('omero.user','root');
>>>>>> p.setProperty('omero.pass','SECRET');
>>>>>> [c,s] = loadOmero(p);
>>>>>> s.getAdminService().getEventContext().groupName
>>>> ans =
>>>>
>>>> default
>>>>
>>>> * You can call session.setSecurityContext after logging in:
>>>>
>>>>>> import omero.model.ExperimenterGroupI
>>>>>> s.setSecurityContext(omero.model.ExperimenterGroupI(0, false));
>>>>>> s.getAdminService().getEventContext().groupName
>>>> ans =
>>>>
>>>> system
>>>>
>>>> * Or you can use s.getAdminService().setDefaultGroup(experimenterObj, groupObj);
>>>>
>>>> which will change persistently which group you log-in as if no "omero.group" value is passed, just as if you had made the change in, say, WebAdmin. However, that shouldn't be done overly frequently, so it's probably best done in one of the UIs.
>>>>
>>>>> - how can I access from within matlab data from collaborators (shared data) in the same group as myself.
>>>> Once you are logged into a group that is collaborative, service methods will begin returning shared data as well as your own, unless the JavaDocs specifically state that it's a method which returns only your own data.
>>>>
>>>>
>>>>> Many thanks,
>>>>> Alex
>>>> Cheers,
>>>> ~Josh.


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