[ome-users] How to remove things from OME database?

[Ilya Goldberg]

There is a delete function for OME available from the command line.  
The delete function can delete a MEX and all of its dependencies (which 
can be a surprising amount).  What's a MEX?  A MEX is central to OME's 
data management.  It stands for Module EXectution.  Everything OME 
keeps track of is the result of a module execution, including image 
import, annotation, analysis, everything.

To use any of the functions in "OME commander", the unix user must also 
be a postgres user (this is why the installer asks for a unix OME admin 
user).
To get help on the delete command:
ome help admin data delete MEX

For example, let's say that you want to delete an image and everything 
that depends on it.  Click in the upper-left corner of a thumbnail in 
the Web UI to get to the Image detail view.  On the right is a list of 
modules that executed on the image.  One of these will be "Image 
import".  Clicking on that will take you to the detail view for that 
MEX.
The MEX ID is the ID in the table at the top.  Let's say its 2.
ome admin data delete MEX -n 2
will show you exactly what will be deleted if you actually did the 
deletion.
ome admin data delete MEX -d 2
will actually delete things (forever, permanently, with no way to get 
them back).

There is a subtle bug here which we're trying to fix:
http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=529
This bug doesn't let you re-import deleted images because it thinks 
they are still in the DB.  What's in the DB is the Original Files that 
served as the inputs for the ImageImport MEX.  The fix for this bug is 
to go ahead and progress through the import chain when importing even 
though the Original Files may already be in the DB.  The tricky part is 
that we still don't want the duplicate image if the image is in fact 
still in the DB.

To really delete the images and the files they came from, you have to 
delete the MEX for the Original Files module.  This is the Input for 
the "Image import" module.  It makes sense, doesn't it?  An image comes 
from some original data files, so these files serve as inputs for the 
image import module.
The OriginalFiles MEX that served as the input for Image import is 
displayed in parentheses in the Module execution column of the Inputs 
table.  Or you can click on the hyperlink and see the detail view for 
the Original Files MEX.  This way, you're taking a step backward 
through the data dependency.

If you delete the Original Files MEX, it will be a completely clean 
deletion and you can re-import those images.  Note that this deletion 
will actually remove these files from OMEIS as well unless you specify 
the -f flag to ome admin data delete MEX.

Ilya

On Jul 13, 2005, at 11:25 AM, Graham Klyne wrote:

> I've created an OME system installation, and the basic image importing 
> seems to work OK .. I can create datasets and browse lists of 
> thumbnails.
>
> Now I've moved the OME installation (and it's virtual machine) to a 
> new location (it's final intended home) and I'm trying to run the same 
> simple tests, but am getting different results like this:
> [[
> Importing images        FINISHED        Imported 0 images from 0 
> files. 1 scanned. 0 unknown format, 1 duplicates, 0 errors.
> ]]
>
> The resulting datasets contains no images (even when I create a new 
> dataset):
> [[
> testproject has 0 images, and is owned by in the OME group.
> It's description is, ""
> ]]
>
> I'm guessing that the database (which was copied with the other files) 
> is now out of phase with the file system data.  How can I reset the 
> database and start over, short of completely reinstalling OME?
>
> Also, is there any way to selectively delete projects and/or images?
>
> #g
>
>
> ---
> Graham Klyne
> Image Bioinformatics Research Group (http://www.bioimage.org/)
> Department of Zoology, University of Oxford
> South Parks Road, Oxford OX1 3PS, UK
> E-mail: <Graham.Klyne at zoo.ox.ac.uk>
> Direct phone: +44-(0)1865-281991
> Departmental fax: +44-(0)1865-310447
>
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