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

[Graham Klyne]

Thanks.

I saw the ome delete MEX command, but didn't realize it applied here.  Your 
explanation is most helpful.

#g
--

At 14:37 14/07/05 -0400, Ilya Goldberg wrote:

>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
>>
>>_______________________________________________
>>ome-users mailing list
>>ome-users at lists.openmicroscopy.org.uk
>>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>_______________________________________________
>ome-users mailing list
>ome-users at lists.openmicroscopy.org.uk
>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

---
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