[ome-users] Batch import of images AND attachments

[Will Moore]

Hi All,

Yes - pixel IDs are returned from the CLI
(doc string confusingly labels this as ImageID in https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/test/integration/library.py#L197 )

Once you have the pixelsId, you can get the imageId and Image like this:
imageId =  conn.getQueryService().get("Pixels", pixelsId).image.id.val
image = conn.getObject("Image", imageId)

  Cheers,

   Will.


On 10 Dec 2013, at 14:35, Josh Moore wrote:

> Hi Graeme,
> 
> On Dec 10, 2013, at 3:32 PM, Graeme Ball wrote:
> 
>> The biggest problem is that the importer does not seem to return the ID of
>> the image after completing the upload, and you need this ID to add your
>> attachments etc.
> 
> The stdout from the CLI importer is the ID of the Pixels objects (as opposed
> to the Image objects). You can also pipe these values to a file for later
> consumption.
> 
> 
>> we wanted to do the same thing, and ended up writing a python script that
>> performs the upload in 2 steps:-
>> 1. upload the images using the command line importer (you can invoke it
>> from python)
>> 2. use the Blitz gateway to add attachments and annotations
> 
> 
> Would you be up for sharing the script?
> 
> Cheers,
> ~Josh
> 
> 
>> Regards,
>> 
>> Graeme
>> 
>> 
>> On Tue, Dec 10, 2013 at 10:26 AM, John Webber (NBI)
>> <John.Webber at nbi.ac.uk>wrote:
>> 
>>> Hi all,
>>> 
>>> 
>>> 
>>> I have been using the command line importer to import images into an Omero
>>> instance as follows:
>>> 
>>> 
>>> 
>>> bin/omero -s $RemoteHost -u "$User" -w "$Password" -p $Port import -d
>>> $Dataset $File
>>> 
>>> 
>>> 
>>> Can anyone let me know if I can also use this format of command to import
>>> ATTACHMENTS to specific images and, if so, please can you advise me of the
>>> correct syntax?
>>> 
>>> 
>>> 
>>> If it is not possible to import attachments to specific images, is anyone
>>> able to recommend how we can do a batch upload of images AND their
>>> attachments, into Omero?
>>> 
>>> 
>>> Thanks
>>> 
>>> John
>>> 
> 
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