OMERO Client Library

Starting to work with the OMERO server is fairly simple from a Java client. Most important is setting up the proper classpath.

Minimum libraries

The client/ directory is available in the binary distribution or can be created from source via java omero build-default. ("<VERSION>" below represent the current value of the particular jar under dist/client).

• OMERO code
  • client/client-<VERSION>.jar
  • client/common-<VERSION>.jar
  • client/model-psql-<VERSION>.jar
• Hibernate annotation dependencies (used by model classes)
  • client/hibernate-annotations-<VERSION>.jar
  • client/hibernate-search-<VERSION>.jar
• JBoss dependencies
  • client/jboss-annotations-ejb3-<VERSION>.jar
  • client/jboss-ejb3-<VERSION>.jar
  • client/jboss-ejb3x-<VERSION>.jar
  • client/jbossall-client-<VERSION>.jar
  • client/jbosssx-<VERSION>.jar
  • client/persistence-api-<VERSION>.jar
• Other
  • client/spring-<VERSION>.jar
  • client/log4j-<VERSION>.jar
  • client/commons-logging-<VERSION>.jar

If you'd like to see the current values for these jars, go to: http://hudson.openmicroscopy.org.uk/job/OMERO/ws/trunk/dist/client/

Using property files

It is often desirable to not hard-code the user name and password nor the server and/or port. In that case, the empty ServiceFactory() constructor can look for properties in several well known locations. Specifically:

• classpath:omero.properties
• classpath:hibernate.properties
• classpath:local.properties
• classpath:jndi.properties

See the OMERO_HOME/etc directory for information on just what properties can be set.

Simple Jython Script : Login, Server, and ServiceFactory

For brevity's sake, a simple example in Jython rather than Java. (One could even also use the Jython console for directly interacting with the server.)

Assuming CLASSPATH has been properly set:

from ome.system import *
from ome.parameters import *

login = Login("name","password")
server = Server("http://myhost")
factory = ServiceFactory( login, server )

id = factory.getAdminService().getCurrentUser().getId()

params = Parameters().addId(id)

myImages = 
factory.getQueryService().findAllByQuery("select i from Image i where i.details.owner.id = :id",params)

For a Java example, see examples/ExampleOne.

Understanding what's going on

Obviously a lot is going on under the hood.

Hashtable env = new Hashtable();
// set properties from Login and Server
Context ctx = new InitialContext(env);
return (IQuery) ctx.lookup(IQuery.class.getName());

...makes calls on the server. In the case of a stateful services, the proxy returned must be held on to for all stateful calls.

Using CLASSPATH.sh from a source build

The build system also provides a bash script (OMERO_HOME/components/<component>/target/generated/resources/Classpath.sh) which will properly set your CLASSPATH environment variable upon being sourced. With CLASSPATH set, it is possible to create simple Java files

vi Test.java
javac -cp $CLASSPATH:. Test.java
java -cp $CLASSPATH:. Test

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See also: OmeroDevelopment, OmeroContributing, OmeroCommunity, examples/ExampleOne