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Changing the schema


OMERO.server stores data in PostgreSQL, a relational database system. The data schema defines what data is stored and how, and new major versions of OMERO may change that schema. Database upgrade scripts transform data from an older version of OMERO so that it conforms to the new schema.

Sometimes, a pull request on GitHub against the develop branch of OMERO may change the code base in ways that cause changes in the resulting database schema. This is a problem because the schema must then be updated, and other developers need to know that code from that pull request may cause problems unless they update their database accordingly. To make sure that these database updates happen when necessary, if your pull request affects the schema then you must increment the database patch number and provide an updated schema as described below.

Changes to the OME-XML model typically require corresponding changes in the OMERO data schema as defined in its XML mappings files. These feed into OMERO’s database schema so this process is then required.

Patch number conflicts

It is possible that another person may also be working on a pull request that changes the schema and increments the database patch number. This is unfortunate because if their pull request is merged it will be as if your pull request does not change the patch number. Others may then unwittingly attempt to use your code with an inappropriate database. If you are considering model changes, it is wise to discuss this with the core OME developers in advance. When working on a schema-changing pull request, first ask or check if yours will be the only one that includes a schema change.

Model object proxies

Changes to model objects that are passed from the server to clients may require corresponding changes to be made to the IceMapper class so that the client-side proxy objects are properly populated.

For example, commit 8815a409 adds fields to the Roles class in the server’s whose instances can be passed to clients via the admin service API so a further commit 2426042a was needed to populate those fields in the proxy object.

Database patch numbers contains a configuration setting for omero.db.patch. An existing OMERO database records the patch number of its schema, as demonstrated from the psql shell:

omero=> select currentpatch from dbpatch;
(1 row)

indicating that a database is on patch version 4. Correspondingly,

$ grep ^omero.db.patch= etc/

By incrementing the patch number with each schema change, OMERO.server is prevented from attempting to use a database whose schema does not match its code.

Updating the schema and the SQL scripts

Users may wish to upgrade their database from an older version of OMERO to one that has your new schema. SQL upgrade scripts are provided to allow users to upgrade easily without having to understand the schema changes themselves, and part of the upgrade script will involve making the schema changes entailed with your pull request. The sql/README.txt file describes where to find the appropriate script for you to adjust. SQL upgrade scripts must be supplied as part of the code changes to upgrade the database from:

  • the last release database, e.g. sql/psql/OMERO5.1DEV__5/OMERO5.0__0,
  • the previous patch’s database, e.g. sql/psql/OMERO5.1DEV__5/OMERO5.1DEV__4.

In your git branch with the code that requires a schema change, edit and increment the value of omero.db.patch. For instance, in the above example, edit the file so that

$ grep ^omero.db.patch= etc/

Move the previous patch’s SQL scripts into their new directory.

$ git mv sql/psql/OMERO5.1DEV__4 sql/psql/OMERO5.1DEV__5

Restore the upgrade to that previous patch.

$ mkdir sql/psql/OMERO5.1DEV__4
$ git mv sql/psql/OMERO5.1DEV__5/OMERO5.1DEV__3.sql sql/psql/OMERO5.1DEV__4/OMERO5.1DEV__3.sql

Build OMERO.server with your code that changes the schema, then use the build-schema build target to update the SQL scripts in the new sql/psql/OMERO5.1DEV__5 directory.

$ ./ build-schema

Now, when you use omero db script in setting up a database for your modified server, the generated SQL script creates the new schema that your code requires. Use this script to set up your database so that you can start OMERO.server and test your changes thoroughly.

A combination of sql/psql/OMERO5.1DEV__4/OMERO5.1DEV__3.sql and the changes within sql/psql/OMERO5.1DEV__5 that git diff reports should help you to create a new sql/psql/OMERO5.1DEV__5/OMERO5.1DEV__4.sql.

When you commit your code and issue a pull request, include the changes to and sql/psql among the commits in the pull request.

Review workflow

Any pull request introducing a schema change will be initially marked and reviewed with a breaking label (see Continuous integration branches and jobs) so after opening your pull request please have it labeled as being breaking. This implies the pull request will first be included in the Breaking jobs and Breaking jobs exclusively. Once positively reviewed, the breaking label will be removed so that the pull request is included in the daily merge builds before final merging.