R/deploy.pbpk.jaqpot.R

In KinkyDesign/JaqpotforR:

# This is JaqpotforR function of jaqpot named 'deploy.pbpk.jaqpot'
# which deploys a pbpk model on 'Jaqpot'.
#
#' deploy.pbpk.jaqpot takes as input the dataframe upon the predictions are made, in
#' order to create the dataset corresponding to the model
#'
#' a covariate model wich calculates physiological parameters based
#' on a patient's characteristics
#'
#'
#' @param dataframe
#' @param odes
#' @param covariate_model

deploy.pbpk.jaqpot <- function(dataframe, covariate_model, odes, comp){
    # basep <- 'http://localhost:8080/'
    # basep <- 'https://api.jaqpot.org/'
    basep <- readline("Base path of jaqpot *etg: https://api.jaqpot.org/ : ")
    username <- readline("Username: ")
    password <- getPass(msg = "PASSWORD: ", noblank = FALSE, forcemask = FALSE)
    loginto <- paste(basep, "jaqpot/services/aa/login/", sep = "")
    print(loginto)
    body <- list(username=username, password = password)
    httr::set_config(config(ssl_verifypeer = 0L))
    res <- POST(loginto, body = body, encode = "form")
    # res <- postForm(loginto, username=username, password=password, style='POST')
    res <- content(res, "text")
    authResponse <- fromJSON(res)
    independentFeaturesfm <- colnames(dataframe)

    title <- readline("Title of the model: ")
    discription <- readline("Discription of the model:")
    algorithm <- 'ODESOLVER'
    libabry_in <- "deSolve"

    predicts <- comp
    predicts[length(predicts)+1] <- "time"
    model <- serialize(list(COVMODEL=covariate_model, ODEMODEL=odes),connection=NULL)
    tojson <- list(rawModel=model,runtime="pbpk-ode", implementedWith=libabry_in,pmmlModel=NULL,independentFeatures=independentFeaturesfm,
                   predictedFeatures=predicts, dependentFeatures=predicts, title=title, description=discription, algorithm=algorithm,
                   additionalInfo =list(comp = comp ))
    json <- toJSON(tojson)
    bearer = paste("Bearer", authResponse$authToken, sep=" ")
    res = POST(basep, path="jaqpot/services/model",
               add_headers(Authorization=bearer),
               accept_json(),
               content_type("application/json"),
               body = json, encode = "json")
    code <- status_code(res)
    if(status_code(res) == 200 ){
      resp <- content(res, "text")
      respon <- fromJSON(resp)
      response <- paste("Model created. The id is: ", respon$modelId, ". Please visit: https://app.jaqpot.org/ to complete ", sep=" ")
      response
    }else{
      code
    }
  }