Tips on Porting your Code to 3.0

Networks

• Most methods in the old CyNetwork should have corresponding methods in the new CyNetwork.

• The new CyNetwork is found in the org.cytoscape.model package.

Attributes

• CyAttrbibutes has been replaces by the concept of CyDataTable.

• Instead of just one, global CyAttributes object, each network has a collection of CyDataTables: for the network, for the nodes, and for the edges.

• For network, nodes, and edges, instead of just one CyDataTable each, we now provide a Map of CyDataTables. The key to the map is a String, or the namespace. For almost all core work, the namespace is defined as CyNetwork.DEFAULT_ATTRS.

• Whereas you used to get an "attribute" using the attribute name, now you get a CyRow in the CyDataTable with a column name. Column name is effectively the same as attribute name.

• To access a row you can call getCyRow(namespace) to get a CyRow object and then call the get(columnName,classType) method.

• The get method includes a Class argument to simplify the interface.

• Since developers will frequently need to get the CyRow for a GraphObject with the default namespace, we've provided a convenience method called attrs(). attrs() is the same as calling getCyRow(CyNetwork.DEFAULT_ATTRS).

• To get the "attribute" named attributeName of a node:

  • Old: CyAttributes.getNodeAttibutes().getStringAttribute(node.getIdentifier(), attributeName);

  • New: node.attrs().get(attributeName,String.class));

Views

Constructors

Spring

• The Spring config files is where all object initialization occurs.
• There are two spring config files:

  • src/main/resources/META-INF/spring/bundle-context.xml

    • This file constructs all "beans" (objects) for this bundle.
    • This file uses references created in bundle-context-osgi.xml to outside services.
    • This file instantiates the "beans" (objects) that are then used to declare services for other bundles to use.

  • src/main/resources/META-INF/spring/bundle-context-osgi.xml

    • This file connects this bundle to the OSGi world which means two things:
    • it creates references that can be used by this bundle from Services provided by other bundles
    • it declares services itself.

• The rule is to keep bundle-context.xml free of any OSGi semantics so that it can be used in a normal spring context and then put all OSGi related XML in bundle-context-osgi.xml.

OSGi

• OSGi impacts the design of Cytoscape, but its APIs are totally hidden through the use of Spring-DM. You should never reference OSGi APIs in your java code. This should all be handled in the Spring XML config files.

• The central concept in OSGi to be aware of is that of a Service.

  • A Service is defined by a java interface. Any valid java interface can be a service.

  • An implementation of this service is simply and implementation of its interface.
  • Access to the service is provided through a service registry.

  • In practice, however, this is all handled by Spring. You do not need to worry about the service registry in your java code!

• From the perspective of the Java developer, a Service is provided in one of two ways:
  1. As an argument to your object's constructor (i.e. it is injected).

  2. Mulitple instances of a service can also be injected into methods in a class. You simply define two methods, an add and a remove method with a signature that includes the interface and a Map of properties:

     • addService( MyServiceInterface s, Map props );

     • removeService( MyServiceInterface s, Map props );

     • These are normal methods in all respects.
     • The Spring xml is configured so that these methods get called when new services are registered or when old services are removed.