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. The repository’s directories contain various files that, together with your SQL database, constitute the information about your users and their data that OMERO.server relies upon for normal operation.

Layout

The repository is internally laid out as follows:

/OMERO
/OMERO/Pixels             <--- Pixel data and pyramids
/OMERO/Files              <--- Original file data
/OMERO/Thumbnails         <--- Thumbnail data
/OMERO/FullText           <--- Lucene full text search index
/OMERO/ManagedRepository  <--- OMERO.fs filesets, with import logs
/OMERO/BioFormatsCache    <--- Cached Bio-Formats state for rendering

Your repository is not:

  • the “database”

  • the directory where your OMERO.server binaries are

  • the directory where your OMERO.client (OMERO.insight or OMERO.importer) binaries are

  • your PostgreSQL data directory

PixelService resolution order for locating binary data for images

When the server is trying to find the binary data for an image, it looks:

  • first under /OMERO/Pixels for a $NUMBER_pyramid file

  • then under /OMERO/Pixels for a regular $NUMBER file

  • then under /OMERO/Files for OMERO 4 files

  • or under /OMERO/ManagedRepository for OMERO 5 files

Locking and remote shares

The OMERO server requires proper locking semantics on all files in the binary repository. In practice, this means that remotely mounted shares such as AFS, CIFS, and NFS can cause issues. If you have experience and/or the time to manage and monitor the locking implementations of your remote filesystem, then using them as for your binary repository should be fine.

If, however, you are seeing errors such as NullPointerExceptions, “Bad file descriptors” and similar in your server log, then you will need to use directly connected disks.

Warning

If your binary repository is a remote share and mounting the share fails or is dismounted, OMERO will continue operating using the mount point instead! To prevent this, make the mount point read-only for the OMERO user so that no data can be written to the mount point.

Changing your repository location

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.

Your repository location can be changed from its /OMERO default by modifying your OMERO.server configuration as follows:

$ omero config set omero.data.dir /mnt/really_big_disk/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:

$ omero admin stop
$ mv /OMERO /mnt/really_big_disk
$ omero config set omero.data.dir /mnt/really_big_disk/OMERO
$ omero admin start

The omero.managed.dir property for the OMERO.fs managed repository may be adjusted similarly, even to a directory outside omero.data.dir.

Note

The managed repository should be located and configured to allow the OMERO server processes fast access to the uploaded filesets that it contains.

Access 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 separate 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   3  omero  omero  4096 Dec 20 10:13 BioFormatsCache
drwxr-xr-x   2  omero  omero  1656 Dec 18 14:31 Files
drwxr-xr-x 150  omero  omero 12288 Dec 20 10:00 ManagedRepository
drwxr-xr-x  25  omero  omero 23256 Dec 10 19:06 Pixels
drwxr-xr-x   2  omero  omero    48 Dec  8  2006 Thumbnails

Repository size

At minimum, the binary repository should be comfortably larger than the images and other files that users may be uploading to it. It is fine to set omero.data.dir or omero.managed.dir to very large volumes, or to use logical volume management to conveniently increase space as necessary.