EpivizServer-class: EpivizServer objects
In epiviz/epivizr-tmp: R Interface to epiviz web app

Description Details Fields Methods Web App Requests Author(s) See Also Examples

This class encapsulates the websocket connection between the R/bioc session and the epiviz web app.

Epiviz uses websockets to connect R/bioc sessions to the epiviz web app. Objects of this class encapsulates websocket objects defined in the httpuv package. The Epiviz session manager defined in class EpivizDeviceMgr calls methods in this class to send requests to the web app or to respond to requests. Requests are created by this class, so actions defined in the JS side are paralleled closely here (this makes the EpivizDeviceMgr) independent of the specifics in the JS side.

port:: Port for websocket connection (default 7312)
websocket:: A WebSocket object from the httpuv package
server:: Internal use only: A server object from the httpuv package, set by the startServer method
interrupted:: Internal use only: has an interrupt been issued
socketConnected:: Internal use only: is the websocket connected
msgCallback:: Internal use only: callback function on websocket message receive, set by bindMgr method
requestQueue:: Internal use only: Queue for unsent requests
tryPorts:: Interval use only: Try more ports when opening websocket server if port requested by user is in use.

: startServer(...): Sets up the server and websocket objects from httpuv package. Specifically, it sets the server field by calling startServer passing port and a set of callbacks, including a onWSOpen callback that sets the websocket field and sets the msgCallback method as the websocket$onMessage callback.
: stopServer(): Stops the websocket server, calling stopServer.
: service(): A blocking loop for the websocket to listen and serve requests. Calls service.
: stopService(): Signals an interrupt so the service loop is stopped.
: runServer(): A convenience function that runs startServer and service. stopServer is called on exit.
: isClosed(): Returns TRUE if server connection is closed
: bindManager(mgr): Sets the msgCallback on websocket message callback. It calls methods from argument mgr, usually an object of class EpivizDeviceMgr. At minimum it must be a list with components verbose and getData.
: sendRequest(request): Converts argument request to JSON and sends through websocket if connected, otherwise, adds to requestQueue.
: sendRequestsInQueue(): Sends all requests currently in the request queue.
: emptyRequestQueue(): Empties request queue.

In all below, requestId is a callback function id set by the session manager.

: addMeasurements(requestId, msType, measurements): adds a set of measurements to the web app. msType indicates the type of measurement, see the typeMap field of EpivizDeviceMgr objects for valid measurement types. measurements is a named character vector of measurement names. names(measuremnts) are the measurement ids.
: rmMeasurements(requestId, measurements, msType): removes a set of measurements. Arguments are as addMeasurements above.
: addChart(requestId, chartType, measurements): adds a chart to the web app. chartType indicates the type of chart to add, see EpivizChart-class for valid chart types. measurements is a character vector containing measurement ids displayed in the chart.
: rmChart(requestId, chartId): removes chart from the web app.chartId specifies the id of the chart to remove. This is returned in response to an addChart request.
: clearChartCaches(requestId, chartIds): clears data caches for given charts. Used when objects in R/bioc session are updated.chartIds is a vector of chart ids.
: navigate(requestId, chr, start, end): Make web app navigate to given genomic region.

Hector Corrada Bravo

EpivizDeviceMgr-class, EpivizChart-class, httpuv, startServer, service, WebSocket

  ## Not run: 
  mgr <- list(getData=function(measurements, chr, start, end) {
                        return(chr)
                      },
              verbose=TRUE)

  server <- epivizr:::EpivizServer$new(port=7123L)
  server$bindManager(mgr)
  server$startServer()
  
  browseURL("http://localhost:7123/")
  tryCatch(server$service(), interrupt=function(int) invisible())
  
## End(Not run)