Open Microscopy Environment

Hi!

I played with the DropBox feature and now have 1500 images imported on accident into omero. How can I delete these images which all appear in orphaned category, but the java application crashes when trying to list and delete them. So how can I delete all orphaned images at once, lets say via command line.

Best,

Sebastian

You could try the webclient.

Orphaned images are visible in the Tree hierarchy, and are paged at 200 images at a time, so you should be able to delete 200 at a time.

If you haven't deployed web yet, you can use the development version directly via instructions: https://www.openmicroscopy.org/site/sup ... ent-server

Hi!

I tried the web interface already without too much success. Actually I forgot a zero, so there are 15000 images to get rid of which takes almost 100 web-pages to click through. Does not sound very convenient to me.

Can't omero delete handle this somehow?

Best,

Sebastian

Hi,

I don't know of a command line option to do what you want. We have a 'delete' command but no query for orphan images on the command line.

One option is to use a small python script:

Code: Select all

from omero.gateway import BlitzGateway

conn = BlitzGateway('will', 'password')
conn.connect()

#print conn.getEventContext()   # if you want to know which group etc you'll be deleting images from
qs = conn.getQueryService()

query = "select obj from Image as obj " \
        "where not exists (select obl from DatasetImageLink as obl where obl.child=obj.id) "\
        "and not exists (select ws from WellSample as ws where ws.image=obj.id)"

imageIds = []

for image in qs.findAllByQuery(query, None):
    print "Deleting :", image.getId().getValue(), image.getName().getValue()
    imageIds.append( image.getId().getValue() )

conn.deleteObjects("Image", imageIds)


Edit this with your own username and password, save this as deleteOrphans.py then:

Code: Select all

$ export PYTHONPATH=$PYTHONPATH:/path/to/omero/lib/python
$ python deleteOrphans.py


Very cool! I had to fix up some little things, but now it works!

Just one thing: If I request thousands of images to be deleted, the server crashes with memory problems. I now only delete a couple of thousand images, then stop the script and start over. This works fantastic!

Thank you very much!

Sebastian

Could you provide us the server log from the time of the memory problems? That should definitely not be happening, even for 10s of 1000s of images.

Thanks,
~Josh