Diff for "Outdated_Cytoscape_3.0/EventHandling"

TableOfContents([2])

Proposal

A lot of hacks are used in the event handling framework in cytoscape 2.x. We don't want 3.0 to look like that, so rethinking the complete framework for firing, listening to and handling events is needed.

Background

Many parts of cytoscape (both 2.6 and 3.0) use the [http://en.wikipedia.org/wiki/Observer_pattern Observer pattern]. There is a consensus that a naive implementation of the observer pattern would not be good enough for two main reasons:

• performance:
  • Since cytoscape has to be able to handle very large networks, firing a seperate event for every single node for a network would cause significant performance problems.
• extra features:
  • Since many parts of cytoscape would be using the same framework for handling events, and events would strongly correspond to state-modification, there is a general consensus that we should try to stuff extra functionality into the event-framework. (The

    consensus is on trying to do this, no one knows whether we will be happy with the result.)

Terminology used on this page

from Effective Java:

• core code is the code that provides a given cytoscape API.

• client code is the code that uses a given cytoscape API.

For example CyNetworkView is 'core code' when talking about the viewmodel API, and 'client code' when talking about the model API. When talking about the model API, CyNetworkView is just something that uses that API, just as a network analysis plugin would. When talking about the model API, CyNtworkView should not be in a special position (more special than being an important usecase; it is certainly not the only usecase.)

We should make the following distinction:

• firing an event is the act of creating the event object and handing it over to the event-framework

• triggering an event is calling a method that results in firing an event

For example, in the current svn trunk, calling CyNetwork.addNode() triggers an AddedNode event, but the firing is done in core code (in the implementation of addNode())

from [http://en.wikipedia.org/wiki/Observer_pattern Observer pattern] terminology:

• Subject is the object whose state-changed the event is about.

• Observer is the object that listens to the event

We also need to talk about

• Actor is the object that triggers the event (for example, a plugin that adds some nodes)

Issues and concerns

The following is an outline of what any solution should consider

Note that we don't have to address all of these at once. (There is a considerable consensus that a 'full solution' is impossible.) It should be pretty explicit which issues a proposal would handle and which it would ignore

1. Batching: The case where many events (like the creation of many nodes) could possibly be grouped together as opposed to handling each one discretely.

   • What does batching mean? In Eclipse a batch is defined as set of nested events:

     It is important to note that the broadcast does not necessarily occur immediately after the method completes. This is because a resource changing operation may be nested inside of another operation. In this case, notification only occurs after the top-level operation completes. For example, calling IFile.move may trigger calls to IFile.create to create the new file, and then IFile.delete to remove the old file. Since the creation and deletion operations are nested inside the move operation, there will only be one notification.

2. Transactions: Actors should leave the model in a valid state, and conflicting changes by different actors prevented. However not everything is editing. Some plugins may be passive, providing a view like an outline, in which case they should not have to concern themselves with the added complexities implied by participating in a transaction. In Eclipse a contributor to a perspective extends/implements either IViewPart or IEditorPart to help make this distinction in roles.

3. Mode: Event handling might have to take into account modes of running like headless, or stateless webserver or statefull web ui

4. Event Object: What information should the event object contain? Using another eclipse example:

   • The resource it corresponds to.
   • The kind of modification (added, removed, or changed).
   • The precise nature of the change (the change flags).
   • A summary of what markers changed on the resource.
   • Deltas for any added, removed, or changed children.

5. OSGI: Event handling should reflect and build on the architecture of OSGI, and may therefore be implemented using the concept of a white board.

6. Abstraction: Plugins should not deal with low-level UI events, e.g. mousePressed, but rather with semantic events that Cytoscape provides, e.g. objectOpened instead of mousePressed() with (e.getClickCount == 2).

   • drag/drop may be a special case. What layer of semantics would Cytoscape want to provide above the Java paradigm of Transferables and DataFlavors?

Dependent design choices

How we design certain parts of 3.0 will be influenced by the design of the event-handling framework. Proposals should consider these as usecases and discuss whether they provide partial solutions for implementing these features. Even if these features are not provided by the event framework 'for free', we should consider how much an approach helps or hinders implementing these

• history
• undo / redo
• provenance tracking

Related projects

• [http://www.eclipse.org/articles/Article-Resource-deltas/resource-deltas.html How you've changed!]

• [http://www.osgi.org/wiki/uploads/Links/whiteboard.pdf OSGI White Boarding]

• [http://cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/ModelDiscussions#head-981c3691f1f46b4149fe9f22ab58a2a310b0e787 Previous Discussion on Event Hanlding]

• [http://wiki.c2b2.columbia.edu/workbench/index.php/Framework geWorkBench framework for event handling]

Prototypes

1. Svn+ssh://Grenache.ucsd.edu/cellar/common/svn/csplugins/trunk/Agilent/creech/BAMEventModel

2.

• http://wodaklab.org/cytoscapeEventAnnotations/xref/index.html (source code)

• http://wodaklab.org/cytoscapeEventAnnotations (maven site)

• http://wodaklab.org/viewvc/svn/cytoscapeEventAnnotations/trunk (browse svn)

• svn co https://wodaklab.org/svn/public/cytoscapeEventAnnotations/trunk (checkout)

Issues

Batching

The problem with batching can be imagined in this way: When deleting a node (especially now that nodes exist w.r.t. only to a model, and not independently of it), listeners need to know about the node AND its context before the node is actually deleted. Thus, in a batch of events, with a naieve implementation, the node would already be gone by the time the batch was received. To circumvent this you might flag the node as being "marked for deletion", but this means, for the duration of the batch, every piece of the code the examines and graph and its nodes, needs to be sensitive to this state. (Updates can present similar issues, but deletion is the best example.)

Why did we want batching? Originally to address the issue of excess "noise". It should be noted that there are ways of reducing noise without batching all events. You, could for instance, just batch similar event types. However the failure to be able to apply a batch to any and all events means concepts like transactions if they are to be arbitrarily defined as a 'unit of work' independently of the code being batched is not possible.

Why not deal with batching later? Because batching (in a transactional sense, or any other higher level abstraction that groups events) does appear to be implementable without making changes to the API, something we wish to avoid in future releases. This is an assumption and it is possible someone might think of a way to introduce batching or transactions later on that don't affect the API, but in building the two prototypes, this does not seem likely.

Do we care about transactions? Isn't easier to leave them out? It is, as we discovered, however that was not our original intuition. We all thought batching would be easy. As well, introducing higher level abstractions about events, like "Undo/Redo" and "Transactions" seems like a natural progression in event handling, like hyper edges and group nodes in graphs. While the need for these things may not exist now, it doesn't seem unreasonable to imagine that we might at some future point, wish we had these capabilities and it is likely that other people will think as we did, that batching is natural extension to event handling, but of course, allowing for it comes with a price. Batching may come at such a price that the trade offs don't make it worth it.

Event Examples

• [:Cytoscape_3.0/EventHandling/EventsIn2.6:]
• [:Cytoscape_3.0/EventHandling/PlannedCoreEventsIn3.0:]

Comments

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