[ome-devel] Accessing OMERO.insight attachements via the API.

[Jerome Avondo]

Hi Jmarie,
 
I still have the problem I described below, I just can't seem to figure out how to take an existing fileannotaion and link it to another image. I always seem to generate the exception below.
 
J.
 
----------------------------------------
> From: jeromeavondo at msn.com
> To: ome-devel at lists.openmicroscopy.org.uk
> Date: Tue, 28 Jul 2009 15:55:04 +0000
> Subject: Re: [ome-devel] Accessing OMERO.insight attachements via the API.
>
>
> Hi Bernhard,
>
> Yes, I had tried the method you showed below as well. Shame issue.
> Hadn't realised the log files were more verbose for error messages. Great tip!
>
> Looking at the logs, it's complaining about duplicate keys for the parent, ie: Image...
> So looks like it thinks the link already exists...
>
> "
> Could not synchronize database state with session
>
> Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "imageannotationlink_parent_key"
> "
>
> But definitely can't see anything in OMERO.insight.
>
> Going to try and look for all the ImageAnnotationLink objects in the database, maybe I when trying a million and one ways I did something to create a bad/corrupt link...
>
> J.
>
> ----------------------------------------
>> From: bernhard.voigt at gmail.com
>> Date: Tue, 28 Jul 2009 15:58:49 +0200
>> Subject: Re: [ome-devel] Accessing OMERO.insight attachements via the API.
>> To: jeromeavondo at msn.com
>> CC: ome-devel at lists.openmicroscopy.org.uk
>>
>> Hi Jerome!
>>
>> Have you tried just creating the link and saving that (python example):
>>
>> link = ImageAnnotationLinkI()
>> link.parent = ImageI(image_id, False)
>> link.child = FileAnnotationI(annotation_id, False)
>> update_service.saveObject(link)
>>
>> You would need to reload the image to get the updated annotation list.
>>
>> Also it's sometimes useful to look at the Blitz0.log file in the
>> var/log folder of the server installation. The error messages are more
>> verbose there and might give a hint what's going wrong in your
>> example. It might not be correct to create the link via linkAnnotation
>> and save the link. I would guess you rather have to save the modified
>> image...
>>
>> Hope that helps! Bernhard
>>
>>
>> On Tue, Jul 28, 2009 at 1:59 PM, Jerome Avondo wrote:
>>>
>>> Hi again,
>>>
>>> Thanks again for the help, I've managed to push forward with all this... But... :)
>>>
>>> I'm now trying to write some methods to copy annotations from one object to the other.
>>> I have no problems with ratings and tags but I'm still finding fileannotations tricky.
>>>
>>> Say I have an image, which already has a fileannotation associated with it. Now I want another Image to have the same fileannotation attached to it as well... I don't want to duplicate the file. Just want the second Image pointing to the same file.
>>>
>>> so I tried,
>>>
>>> using the loadAnnotations() from the IMetadataPrx object, to get all annotations for my ImageID and of type ome.model.annotations.FileAnnotation. Which seems to work fine as I can get to the data that way.
>>>
>>> Then I try to set the retrieved FileAnnotation objects to my second Image object, using the Image member function, linkAnnotation(), to create a ImageAnnotationLink which I then save the new link to the database via the gateway saveObject(). But this doesn't work.
>>>
>>> When I try and save the link, I get, message = "could not insert: [ome.model.annotations.ImageAnnotationLink]; nested exception is org.hibernate.exception.ConstraintViolationException:"
>>>
>>> I also tried creating a new FileAnnotation object, and pointing it to the OriginalFile of the retrieved FileAnnotation. Still same error, when saving the link.
>>>
>>> And I also tried retrieving the FileAnnotation or OriginalFile objects by their ids via queries, thinking I might not have the full objects loaded, but same issue...
>>>
>>> Running out of ideas, any help welcome....
>>>
>>> Thanks,
>>>
>>> J.
>>>
>>> ________________________________
>>>> CC: ome-devel at lists.openmicroscopy.org.uk
>>>> From: j.burel at dundee.ac.uk
>>>> Subject: Re: [ome-devel] Accessing OMERO.insight attachements via the API.
>>>> Date: Wed, 22 Jul 2009 16:14:58 +0100
>>>> To: jeromeavondo at msn.com
>>>>
>>>>
>>>> Hi Jerome
>>>>
>>>> If you want to remove the tag, you need to delete the link.
>>>> We should add some methods to the API to improve the usability
>>>>
>>>> Retrieve the link using the findByQuery of the IQuery service i.e.
>>>> query =
>>>> "select link from ImageAnnotationLink as link where " +
>>>> "link.parent.id = :imageID and link.child.id =: tagID";
>>>>
>>>> then delete the link
>>>> using the deleteObject method from the IUpdate service.
>>>>
>>>> Hope it helps
>>>>
>>>> Jmarie
>>>
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