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This module, intended for use within Apache Isis, provides an implementation of the DataNucleus PersistenceManagerFactory class. This uses Flyway API to automatically apply any database migration scripts prior to the bootstrapping of the rest of the Apache Isis runtime.


The integration provided by this module runs a single instance of Flyway for the entire database, even if that database has multiple schemas (as is common in Apache Isis applications). In other words (although Flyway as a tool supports it), this integration does not allow for the tables in different schemas to have their own separate migration history.

How to run the Demo App

The prerequisite software is:

  • Java JDK 7 or JDK 8

  • maven 3 (3.3.x is recommended).

To build the demo app:

git clone
mvn clean install

To run the demo app:

mvn -pl webapp jetty:run

The app will bootstrap against an in-memory database, however it will be Flyway that sets up the database schema (rather than DataNucleus automatically creating the database as might normally be the case). This is discussed in a little more detail below.

Then log on using user: sven, password: pass

What happens during bootstrapping

When the application bootstraps, it uses the run two DB migration files that reside in db.migration package of the webapp module:

As a side-effect of running the migration, the flyway DB schema management tables are created.


While (for simplicity) the demo application uses files named V1__, V2__ and so on, we recommend you use a more sophisticated naming convention based on dates. See below for further discussion.

All of this can be confirmed by invoking Prototyping > HSQL DB Manager to spawn off a Swing UI client that can view the (in-memory) database:


This shows the migration scripts have been run, and the Flyway schema tables created and populated.

How to Configure

To configure:

  • update your classpath by adding this dependency in your project’s webapp module’s pom.xml:

  • In the webapp's file, set:


Disabling DataNucleus' autoCreateAll property in turn enables Flyway migrations.


Using autoCreateTables=false (instead of autoCreateAll) will also enable Flyway migrations, but will continue to allow DataNucleus to (re)create table constraints; see the section below for further discussion.

Enabling DataNucleus' validateAll property means you can be assured that your migration scripts have brought the database schema into the same shape as is expected by DataNucleus; if there is a mismatch then the app will fail to bootstrap.


See the section below for workarounds when validation errors are thrown that should not be.

The flyway.schemas property is intended to list all of the schemas that Flyway manages as a single indivisible set of tables; the schema_version table will be created in the first schema listed. If these schemas do not exist already then Flyway will automatically create them in the current database; however if any of them do exist then Flyway will not create any of the schemas.

If any of the tables that need to be managed happen to reside in a default schema (such as "dbo" for SQL Server, or "PUBLIC" for HSQLDB), then either:

  • do not list that default schema within flyway.schemas, and also do not provide migration scripts to create the schemas themselves (relying on Flyway to create the schemas instead), or

  • do list that default schema within flyway.schemas, and then do provide migration scripts to create the schemas themselves, or

  • just list "flyway" as the one and only schema in flyway.schemas, and then do provide a migration scripts to create the schemas.

    This will have the result of creating a new flyway.schema_version table.

Of these options, the demo application for this module goes with the last approach.


Flyway’s migrate command supports a large number of other configuration options. All of these can be enabled/set using a property name consisting of isis.persistor.datanucleus.impl. prefix along with the property as a suffix.

How to Use

The sections below describe some of the common use cases when using Flyway to manage database migrations.

Naming convention for scripts

When Flyway runs it searches for files named Vnnnn__, where nnnn is some number. In the Flyway documentation (and, for that matter, in the demo app for this module), those numbers start at 1. However, if your team uses feature branches then this is likely to cause conflicts when those feature branches are merged back into master/trunk.

Luckily, Flyway does not require the version numbers to be contiguous; moreover the number can contain '_' or '.' as a separator. Therefore, (along with others) we recommend that the number used is the current date/time, for example:


When the feature branches are merged, you (the developer) should check that any new migrations have a later timestamp than the version of the current production database; chances are they will be. But if necessary, the filename/timestamp can be updated, eg to be the current date/time that the merged is performed.

Alternatively, an "out-of-order" migration (as discussed below) could be used.

Disabling for development

When developing Apache Isis applications, it’s common practice to prototype and run integration tests in memory, by default using HSQLDB. In production, however, some other database will most likely be used (PostgreSQL, MySQL, MS SQL Server etc).

Now Flyway - by design - does not attempt to abstract over different database vendors. In other words, the SQL migration scripts that are designed for production will quite possibly not work for development environment. The long and short of this is that you will most likely want to simply disable the flyway migration when running in-memory against HSQLDB.

This can be done simply by setting either the autoCreateAll or the autoCreateTables property back to true, either in the file, eg:


Or, (if using mvn jetty:run or org.apache.isis.WebServer) with a system property, eg:

mvn jetty:run -Disis.persistor.datanucleus.impl.datanucleus.schema.autoCreateAll=true

Flyway migrations are not disabled if only autoCreateConstraints property is enabled. This enables the use case for dropping all constraints prior to migration, and then having DataNucleus recreate them after. See below for further discussion.

Idempotent constraints

As part of the release process, some DBAs prefer to drop all database constraints, then recreate them at the end of the release. This helps ensure that what is deployed to the database is only what should be there.


Obviously this isn’t feasible for very large databases; in such cases dropping only foreign key/alternate indices (but not primary keys) may be more appropriate.

To effect this:

  • dropping constraints can be done using the "before migrate" callback from Flyway.

    Create a script beforeMigrate.sql which will drop all these objects, place in db.migration package alongside any other migration scripts.

  • recreating constraints can be done using DataNucleus' autoCreateConstraints property.

    In webapp module’s file, also set:


When the application is bootstrapped, Flyway will run the beforeMigrate.sql script to drop all constraints and other objects, and then DataNucleus will reinstate those constraints as it initializes.

Managing views etc

In addition to the tables that support an Apache Isis application, there may be additional artifacts such as views and stored procedures that also need to be deployed. For example, such views might be to support third-party reports or other similar tools.

Since such views may need to be updated whenever the underlying tables change, it makes sense to manage them as part of the codebase of the Apache Isis application.

On the other hand, since these are not part of the application, DataNucleus cannot be used to automatically create these artifacts. Instead, Flyway’s repeatable migrations can be used to run the scripts.

A repeatable migration is simply a file with the prefix R__, residing in the db.migration package as usual; for example R__reporting-views.sql. Typically these scripts should drop all views and then recreate them; ie they should be idempotent.

Flyway will run these scripts whenever they file is changed (it maintains a checksum of the file).

(Manual) baselining an existing database

If you want to start using Flyway for with an existing database that is already in production, then it must be baselined.

This involves Flyway creating its schema_version table, and inserting a row to represent the "current" version of that database. Thereafter only scripts with a number higher than that version will be applied.

As a minimum, baselining involves simply running the baseline command:

flyway -driver=... \
       -url=... \
       -user=... \
       -password=... \
       -baselineVersion="yyyyMMdd.hhmm" \
       -baselineDescription="Initial take-on" \

where yyyyMMdd.hhmm can be the current date/time.


It’s also possible to specify command-line options using a flyway.conf configuration file.

If you wish, you could also generate scripts to represent the current state of the database. These won’t be used by Flyway in the baselined system, but could be used to start the app against a completely empty database (if Flyway isn’t otherwise disabled).

For example, scripts can be geneated for MS SQL Server using the Generate and Publish Scripts wizard (Tasks > Generate Scripts); save these as VyyyyMMdd.hhmm__initial-take-on.sql. This follows the date/time naming convention discussed above.

More advanced use cases

And here are some slightly more advanced use cases to consider.

(Automatic) baselining an existing database

Rather than manually baselining an existing (production) database, Flyway also supports automatic baselining. With this option enabled, if Flyway is run against a database with no schema_version table, then it will automatically create that table and populate it with a single baseline row.

This can be configured by updating the webapp module’s file:


Change the flyway.baselineVersion if you want some other value to be used as the baseline version.

Handling validation errors

Sometimes validateAll can result in DataNucleus throwing an exception even if the actual database matches the schema. The underlying reason for this occurring will vary; one reason is a buggy JDBC driver misreporting database metadata. It is however possible to workaround this issue.

By way of example, when running against MS SQL Server you may find that BLOB/CLOB columns are reported as being invalid. One common example is the CommandJdo entity (in the Isis addons' command module), with its exception and a memento properties. This is defined as:

public class CommandJdo {
    @javax.jdo.annotations.Column(allowsNull="true", jdbcType="CLOB")
    private String exception;
    @javax.jdo.annotations.Column(allowsNull="true", jdbcType="CLOB")
    private String memento;

In MS SQL Server this is mapped to a table with a column of type TEXT. However, this results in DataNucleus throwing an exception, to the effect that the datastore defines a LONGVARCHAR, while the (class) metadata defines a CLOB.

The workaround is to redefine the JDO metadata using an .orm file. For example, CommandJdo can be made to work by adding CommandJdo-sqlserver.orm:

<?xml version="1.0" encoding="UTF-8" ?>
<orm xmlns=""

    <package name="org.isisaddons.module.command.dom">
        <class name="CommandJdo"
            <property name="exception">
                <column name="exception" jdbc-type="CLOB" sql-type="LONGVARCHAR" allows-null="true"/>
            <field name="memento">
                <column name="memento" jdbc-type="CLOB" sql-type="LONGVARCHAR" allows-null="true"/>


This should reside in the appropriate package (org.isisaddons.module.command.dom in this case).

Another example is the DocumentAbstract entity (in the Incode catalogs' document module), with its blob_byte and a memento properties.

public class DocumentAbstract {
    @javax.jdo.annotations.Column(allowsNull = "true", name = "blob_bytes", jdbcType = "BLOB", sqlType = "BLOB")
    private byte[] blobBytes;
    @javax.jdo.annotations.Column(allowsNull = "true", name = "clob_chars", jdbcType = "CLOB", sqlType = "CLOB")
    private String clobChars;

The fix in this case is the following DocumentAbstract-sqlserver.orm file:

<?xml version="1.0" encoding="UTF-8" ?>
<orm xmlns=""

    <package name="">
        <class name="DocumentAbstract"
            <field name="blobBytes">
                <column name="blob_bytes" jdbc-type="BLOB" sql-type="LONGVARBINARY" allows-null="true"/>
            <field name="clobChars">
                <column name="clob_chars" jdbc-type="CLOB" sql-type="LONGVARCHAR" allows-null="true"/>

The last thing to do is to instruct DataNucleus to also read these additional .orm files. This can be done using:


where sqlserver matches the filename (DocumentAbstract-sqlserver.orm and so on).

Out-of-order migrations

Sometimes it is necessary to run "outOfOrder" migrations; that is, to run a migration whose number is less than that of the current production database.

To enable this feature, add the following to the webapp module’s file:


Java-based migrations

In addition to SQL-based migrations, Flyway also supports migrations implemented in Java. These follow the same naming convention as SQL-based migrations, and also reside in the db.migration package. Of course, they must be compiled and reside on the classpath, very similar to Apache Isis fixture scripts.

Database vendor-specific scripts

Flyway does not In addition to SQL-based migrations, Flyway also supports migrations implemented in Java. These follow the same naming convention as SQL-based migrations, and also reside in the db.migration package. Of course, they must be compiled and reside on the classpath, very similar to Apache Isis fixture scripts.

A process for creating migration scripts

Suppose you’ve developed a new feature which will require a database schema change; how should the migration scripts be created and tested? Here’s one approach:

  • obtain a backup of the current production database (which is already under Flyway’s control; baseline it if not)

    In fact, all that is required is the schema of this database. So, as a minor refinement, you could set up a CI pipeline that hooks onto your nightly database backups; this would restore the production database to some scratch DB, then truncate all tables, then creates a backup of that truncated database.


    See truncate-all-tables.sql for a script that does this for MS SQL Server.

  • in your development environment, restore the current production database (or truncated version) twice:

    • restore once to current DB

    • restore another to test DB

  • create a completely blank dev DB

    You could either create an empty database, or zap an existing scratch DB.


    See drop-all-tables.sql for a script that does this for MS SQL Server.

  • run app against this empty dev database, with autoCreateAll=true

    This disables Flyway, causing DataNucleus to create the schema based on its current metadata

  • next, use a comparison tool to compare current against dev.


    One option is to use the command line tools provided by liquibase (itself a DB migration framework that "competes" with Flyway; here we just leverage its diff utility). See below for details of how to use liquibase’s commandline tool.

  • Save SQL scripts capturing the difference

  • Finally, run app against test DB, this time with Flyway re-enabled and with DataNucleus validation re-enabled also:

    • autoCreateAll=false (or autoCreateTables=false) re-enables Flyway, causing it apply the migration scripts

    • validateAll=true causes DataNucleus to check that the resultant DB schema matches that required by the entity metadata.

If there is an issue then the app will fails to start; use the errors in the console to diagnose the issue and then go round the loop.

Using Liquibase to diff databases

Liquibase is another Java-based migration tool that "competes" with Flyway; its scope is rather broader than Flyway which some prefer. Here we just leverage its diff utility in order to help generate migration scripts.

The shows how this can be done for a SQL Server database. It is invoked as follows:



(Referring back to the process described above) this compares the current production database to the development database.

The script uses a schema.txt file which lists all of the database schemas to compare. This should the same list of schemas as configured in (the flyway.schemas property), described above. Adjust as necessary.

Obviously, the above script requires that liquibase shell script is on your $PATH (or liquibase.bat on your %PATH%).

Known issues

None currently

Change Log

  • 1.14.0 - released against Isis 1.14.0

  • 1.13.1 - Extending to support flyway properties (eg outOfOrder, baselineOnMigrate), allow DN to recreate constraints, support multiple DBs; docs on repeatable migrations and other features

  • 1.13.0 - First release, against Apache Isis 1.13.0


Copyright 2016-date Dan Haywood

Licensed under the Apache License, Version 2.0 (the
"License"); you may not use this file except in compliance
with the License.  You may obtain a copy of the License at

Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
KIND, either express or implied.  See the License for the
specific language governing permissions and limitations
under the License.


There are no third-party dependencies.

Maven deploy notes

Only the dom module is deployed, and is done so using Sonatype’s OSS support (see user guide).

Release to Sonatype’s Snapshot Repo

To deploy a snapshot, use:

pushd dom
mvn clean deploy

The artifacts should be available in Sonatype’s Snapshot Repo.

Release an Interim Build

If you have commit access to this project (or a fork of your own) then you can create interim releases using the script.

The idea is that this will - in a new branch - update the dom/pom.xml with a timestamped version (eg It then pushes the branch (and a tag) to the specified remote.

A CI server such as Jenkins can monitor the branches matching the wildcard origin/interim/* and create a build. These artifacts can then be published to a snapshot repository.

For example:

sh 1.14.0 origin


  • 1.14.0 is the base release

  • origin is the name of the remote to which you have permissions to write to.

Release to Maven Central

The script automates the release process. It performs the following:

  • performs a sanity check (mvn clean install -o) that everything builds ok

  • bumps the pom.xml to a specified release version, and tag

  • performs a double check (mvn clean install -o) that everything still builds ok

  • releases the code using mvn clean deploy

  • bumps the pom.xml to a specified release version

For example:

sh 1.14.0 \
              1.15.0-SNAPSHOT \
              "this is not really my passphrase"

where * $1 is the release version * $2 is the snapshot version * $3 is the email of the secret key (~/.gnupg/secring.gpg) to use for signing * $4 is the corresponding passphrase for that secret key.

Other ways of specifying the key and passphrase are available, see the `pgp-maven-plugin’s documentation).

If the script completes successfully, then push changes:

git push origin master && git push origin 1.14.0

If the script fails to complete, then identify the cause, perform a git reset --hard to start over and fix the issue before trying again. Note that in the dom's pom.xml the nexus-staging-maven-plugin has the autoReleaseAfterClose setting set to true (to automatically stage, close and the release the repo). You may want to set this to false if debugging an issue.

According to Sonatype’s guide, it takes about 10 minutes to sync, but up to 2 hours to update search.

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