OMERO.server Binary Repository
About
The OMERO.server binary data repository is a fundamental piece of server-side functionality. It provides optimized and indexed storage of original file, pixel and thumbnail data, attachments and full text indexes. Its structure is based on OMEIS.
Layout
The repository is internally laid out as follows:
/OMERO
/OMERO/Pixels <--- Pixel data
/OMERO/Files <--- Original file data
/OMERO/Thumbnails <--- Thumbnail data
/OMERO/FullText <--- Lucene full text search index
Permissions
Your repository should be owned by the same user that is starting your OMERO.server instance. This is often either yourself (find this out by executing whoami
) or a seperate omero
(or similar) user who is dedicated to running OMERO.server. For example:
$ whoami
omero
$ ls -al /OMERO
total 24
drwxr-xr-x 5 omero omero 128 Dec 12 2006 .
drwxr-xr-x 7 root root 160 Nov 5 15:24 ..
drwxr-xr-x 2 omero omero 1656 Dec 18 14:31 Files
drwxr-xr-x 25 omero omero 23256 Dec 10 19:06 Pixels
drwxr-xr-x 2 omero omero 48 Dec 8 2006 Thumbnails
Your repository is not
-
The "database"
-
The directory where your OMERO.server binaries are
-
The directory where your OMERO.client (OMERO.insight, OMERO.editor or OMERO.importer) binaries are
-
Your PostgreSQL data directory
-
A place to store moldy sandwiches
Changing your repository location
Your repository location can be changed from it's /OMERO
or C:\OMERO
default by modifying your OMERO.server configuration as follows (remembering that Windows C:\
style paths must have backslashes escaped):
cd omero-Beta4.0.0
bin/omero config set omero.data.dir /mnt/really_big_disk/OMERO
cd C:\omero-Beta4.0.0
bin\omero config set omero.data.dir D:\\OMERO
The suggested procedure is to shut down your OMERO.server instance, move your repository, change your omero.data.dir
and then start the instance back up. For example:
cd omero-Beta4.0.0
bin/omero admin stop
mv /OMERO /mnt/really_big_disk
bin/omero config set omero.data.dir /mnt/really_big_disk/OMERO
bin/omero admin start
cd C:\omero-Beta4.0.0
bin\omero admin stop
move C:\OMERO D:\
bin\omero config set omero.data.dir D:\\OMERO
bin/omero admin start
NOTE: It is strongly recommended that you make all changes to your OMERO binary repository with the server shut down. Changing the omero.data.dir
configuration does not move the repository for you, you must do this yourself.