Synapse Client for Cytoscape

For details on what this app does, check out the app page: http://apps.cytoscape.org/apps/synapseclient

Key classes

• SynClient.java

  Issues requests to the Synapse web service. Requests are encapsulated as Cytoscape tasks.

  This class does not use the Java client library provided by Synapse, as it doesn't provide the means to cancel HTTP requests nor the means to monitor the progress of requests. These limitations prevent their client library from being able to be tied into Cytoscape's task structure. This class addresses these limitations and acts as a replacement for the client Java library provided by Synapse.

• BrowserDialog.java

  This is the main Swing UI dialog for this app.

  Most tasks have the static method noTunables. This method is used by BrowserDialog. For instance, ImportNetworkFromSynapseTask has a tunable for the Synapse entity ID. In the browser dialog, when the user selects an entity, the BrowserDialog calls noTunables, as it already knows the entity's ID.

How authentication works

1. The user goes to the Apps menu and chooses Synapse. This starts the BrowseTask.
2. SynClientMgr maintains an instance of SynClient. The BrowserTask sees if there's a valid SynClient instance. If there is, the user is already logged in and proceeds to open the browser dialog.
3. If there is no valid SynClient instance, the user isn't logged in. The BrowseTask opens the login dialog.
4. When the user clicks OK in the login dialog, BrowseTask creates an instance of SynClient using a new APIAuthKey with the provided user credentials. It then calls SynClient.newUserProfileTask and runs the task.
5. If the task succeeds, the user's credentials are correct. It registers the new instance of SynClient with SynClientMgr. This closes the login dialog and opens the browser dialog.
6. If the task fails, the login dialog shows an error message.

How the entity types are detected

When the user selects an entity in the browser dialog, the browser dialog determines whether the entity can be imported as a network, table, or session. How does this work?

ImporterMgr maintains a collection of all InputStreamTaskFactorys registered in OSGi. It extracts each InputStreamTaskFactory's CyFileFilter, which specifies the file types supported by a given InputStreamTaskFactory. BrowserDialog calls ImporterMgr.doesImporterExist with the entity's extension and either NETWORK, TABLE, or SESSION for DataCategory. If ImporterMgr finds an InputStreamFactory that supports the given file extension and DataCategory, it will return true. The browser dialog will then add an import button for the given DataCategory.