#'Created on Jun 4, 2018
#'Updated on May 4, 2020
#'Script example to generate disGeNET networks data in Cytoscape from R.
#'Before executing the script, you must have Cytoscape running and the disGeNET-App installed 
#'(you don't need to start disGeNET app).
#'Requires the httr library.

library(httr)

#' Creates a valid REST url for the REST call to the disGeNET automation module.
#' @param netType A string containing the type of the network to be created.
#' @param host The host of the url, by default 127.0.0.1 (localhost). To change the host do it manually.
#' @param port The listening port, by default 1234. To change the port do it manually.
#' @param version The version of the automation module, by default v7.
#' @return url A string in url format, with the given parameters.
#' @author jsauch
disgenetRestUrl<-function(netType,host="127.0.0.1",port=1234,version="v7"){
  if(is.null(netType)){
    print("Network type not specified.")
  }else{
    url<-sprintf("http://%s:%i/disgenet/%s/%s",host,port,version,netType)
  }
  return (url)
}

#'Executes a REST call to the disGeNET automation module in Cytoscape and retrieves the operation result.
#'This function builds the url for the rest call automatically with the default values.
#'@param netType A string containing the type of the network to be created.
#'@param params A list with the params for the network. Check the possible params in the Swagger UI of cytoscape.
#'@return result A list with the results of the operation.
#'@author jsauch
disgenetRestCall<-function(netType,netParams){
  url<-disgenetRestUrl(netType)
  restCall<-POST(url, body = netParams, encode = "json")
  result<-content(restCall,"parsed")
  return(result)
}

#Example of params for the gene-disease network.
geneDisParams <- list(
  source = "UNIPROT",
  assocType = "Genetic Variation",
  diseaseClass = "Neoplasms",
  diseaseSearch = " ",
  geneSearch = " ",
  initialScoreValue = "0.0",
  finalScoreValue = "1.0"
)

#Example of params for the variant-disase network.
variantDisParams <- list(
  source= "UNIPROT",
  assocType= "Genetic Variation",
  diseaseClass= "Neoplasms",
  diseaseSearch= " ",
  geneSearch= " ",
  variantSearch= " ",
  initialScoreValue= "0.0",
  finalScoreValue = "1.0",
  showGenes= "true"
)

#Generate the gene-disease network, and show the resuland show the results.ts.
geneDisResult <- disgenetRestCall("gene-disease-net",geneDisParams)

#Generate the variant-disease network, and show the results.
 variantDisResult <- disgenetRestCall("variant-disease-net",variantDisParams)
 variantDisResult