R/ndex_networks.r

In frankkramer-lab/ndexr: NDEx R client library

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## Authors:
##   Alex Ishkin [aleksandr.ishkin@thomsonreuters.com]
##   Dexter Pratt [depratt@ucsd.edu]
##   Frank Kramer [frank.kramer@informatik.uni-augsburg.de]
##   Florian Auer [florian.auer@informatik.uni-augsburg.de]
##
## History:
##   Created on 6 June 2014 by Ishkin
##   Split on 25 January 2017 by Auer
##     
## Description:
##    Contains functions to search and retrieve networks
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###
###   Network Functions
###
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#' Search networks in NDEx (by description)
#' 
#' This functions searches the public networks on an NDEx server for networks containing the supplied search string. T
#' his search can be limited to certain accounts as well as in length.
#' 
#' @param ndexcon object of class NDExConnection link{ndex_connect}
#' @param searchString string by which to search
#' @param accountName string (optional); constrain search to networks administered by this account
#' @param start integer (optional); specifies that the result is the nth page of the requested data. The default value is 0
#' @param size integer (optional); specifies the number of data items in each page. The default value is 100
#' 
#' @return Data frame with network information: ID, name, whether it is public, edge and node count; source and format of network. NULL if no networks are found.
#' 
#' @section REST query:
#' GET: ndex_config$api$search$network$search
#' @note Compatible to NDEx server version 1.3 and 2.0
#' @note Search strings may be structured
#' 
#' @examples 
#' ndexcon = ndex_connect()
#' networks = ndex_find_networks(ndexcon,"p53") 
#' @export
ndex_find_networks <- function(ndexcon, searchString="", accountName, start, size){
  
  if (missing(start)) start = NULL
  if (missing(size)) size = NULL
  
  ##Form JSON to post
  query = list(searchString=searchString)
  if (!missing(accountName)){
    query$accountName=accountName
  }
  query <- jsonlite::toJSON(query, auto_unbox = TRUE)
  
  ##Form route
  ## ToDo: somehow the 1.3 api changed?! old version:
  ## route <- sprintf("/network/search/%s/%s", start, size)
  ## now somehow it changed to "http://public.ndexbio.org/rest/network/textsearch/0/1000" (from Chrome, 28.Nov.2016)
  api = ndex_helper_getApi(ndexcon, 'search$network$search')
  route <- ndex_helper_encodeParams(api$url, api$params, start=start, size=size)
  
  ##Get a list of NetworkSummary objects
  response <- ndex_rest_POST(ndexcon, route=route, data=query)
  response = response$networks

  if(length(response) > 0){
    return(response)
  } else {
    return(NULL)
  }
}