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Database Upgrades

When necessary and appropriate, the OMERO team provides database upgrades which can be applied from the command line. These scripts are found under source:trunk/sql/psql followed by directories named after the current database version, which can be found in source:trunk/etc/omero.properties .

Upgrade scripts are not provided between all consecutive versions, since intermediate versions are developer releases, and it is assumed that the developers work from a fresh database.

All public releases are accompanied by an upgrade script if necessary.

Database version

The naming scheme is not linear but rather hierarchical to support branching between various sites. The first part of name, the database version is a string name like OMERO3 or OMERO3A. The second part of any name is the patch level and is a simple counting integer.

The versions for a given OMERO release are defined in OMERO_HOME/etc/omero.properties:

omero.version=3.0-TRUNK
omero.dbversion=OMERO3
omero.dbpatch=5

omero.version describes the software version, and is further unimportant for database upgrades. omero.dbversion and omero.dbpatch, however, determine which version of the database the OMERO server expects to find. During startup, they are tested against the dbpatch table.

Dbpatch

If the dbpatch table is not present, an InternalException will be thrown with the following message:

***************************************************************************************
Error connecting to database table dbpatch. You may need to bootstrap.
See https://trac.openmicroscopy.org.uk/omero/wiki/DbUpgrade
***************************************************************************************

If all else is configured properly, this most likely is due to the use of database created before r1547. If this is the case you will need to use the OMERO3__5__bootstrap.sql script to create a dbpatch table in your database.

Otherwise, the latest values for the db version and db patch are retrieved via:

select currentversion, currentpatch from dbpatch order by id desc limit 1

and compared to the values in omero.properties. If there is a mismatch, an InternalException will be thrown with the following message:

***************************************************************************************
DB version (OMERO3__0) does not match omero.properties (OMERO3__5). Please apply a db upgrade.
See https://trac.openmicroscopy.org.uk/omero/wiki/DbUpgrade
***************************************************************************************

which requires a db upgrade.

Upgrading

Currently, there is no automatic way to upgrade a database. Rather, the SQL scripts under OMERO_HOME/sql/psql can be used to move from one version to the next. For example, if you are on OMERO3__5 and would like to get to the OMERO3_7, then you can use

then you can use:

cat OMERO3__5__OMERO3__6.sql OMERO3__6__OMERO3__7.sql | psql DATABASENAME

to upgrade.

Full example

$ psql omero3
omero3=#  select currentversion||'__'||currentpatch from dbpatch order by id desc limit 1;
 ?column?  
-----------
 OMERO3__5
(1 row)

$ cd $OMERO_HOME
$ grep omero.db etc/omero.properties 
omero.dbversion=OMERO3
omero.dbpatch=5

$ cd sql/psql
$ cat OMERO3__5__OMERO3__6.sql OMERO3__6__OMERO3__7.sql | psql omero3

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