That should be no problem. The config below is not tested, but should work and give you an idea how to set it up.
<neo4j:config graphDatabaseService="gds"/>
<bean id="gds" class="...EmbeddedGraphDatabase">
<constructor-arg value="target/graph-db"/>
</bean>
<bean id="serverWrapper" class="...WrappingNeoServerBootstrapper" init-method="start" destroy-method="stop">
<constructor-arg ref="gds"/>
</bean>
Transactions are handled the same way as the Neo4j-REST API does it. One per request. The underlying neo4j-rest-graphdb library also supports the REST-Batch API but that is not yet leveraged in SDN.
Update:
Please also add the dependency for the webadmin static files to your project, something like this:
<dependency>
<groupId>org.neo4j.app</groupId>
<artifactId>neo4j-server</artifactId>
<version>1.5</version>
<type>jar</type>
<classifier>static-web</classifier>
</dependency>
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