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. 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 JBoss. This is often either yourself (find this out by executing whoami) or a seperate jboss (or similar) user who is dedicated to running OMERO.server. For example:

$ whoami
jboss
$ ls -al /OMERO
total 24
drwxr-xr-x  5 jboss  jboss   128 Dec 12  2006 .
drwxr-xr-x  7 root    root   160 Nov  5 15:24 ..
drwxr-xr-x  2 jboss  jboss  1656 Dec 18 14:31 Files
drwxr-xr-x 25 jboss  jboss 23256 Dec 10 19:06 Pixels
drwxr-xr-x  2 jboss  jboss    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 and/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 the etc/omero.properties file in your extracted OMERO.server directory as follows:

omero.data.dir=/mnt/really_big_disk/OMERO

NOTE: Please remember that once a change has been made to etc/local.properties or etc/omero.properties you must follow the instructions on the OmeroInstall page under Reconfiguration and perform a server restart.

NOTE: Also remember that once you have changed your repository location you must move the previous omero.data.dir content to the new location. For example:

mv /OMERO /mnt/really_big_disk/OMERO

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See also: OmeroInstall, OmeroInstallWindows