R/ag_manpractices.R

In AGROFIMS/ragapi: An R-implementation of the Agronomy API standard (AgAPI) used by Agronomy Fieldbook Management System (AGROFIMS) platform

#' @include checkers.R utils.R
#' 
#' Management Measurements Class
#' 
#' @description Class to represent Management measurements data from AgroFIMS. It inherents from AgAPI client class 
#' all the basic parameters and methods.
#'
#' @title AgManPrac
#'
#' @docType class
#'
#' @format R6 class
#'
#' @field user specifies the user name, defaults to NULL 
#' @field password specifies the password, defaults to NULL
#' @field user specifies the user name, defaults to NULL 
#' @field password specifies the password, defaults to NULL
#' @field authentication specifies the password, defaults to NULL
#' @field token specifies the password, defaults to NULL
#' @field user_agent specifies the password, defaults to NULL
#' @field serverURL specifies the password, defaults to 
#'                  http://research.cip.cgiar.org/agrofims/api/dev/
#' @field version specifies the version, defaults to 0051
#' @field endPoint specifies the end point value,   tableName/method.php 
#' @importFrom R6 R6Class
#' 
#' @export
#' 
AgManPrac <- R6::R6Class(
  
  classname = "AgManPrac",
  inherit = AgAPIClient,
  # private = list(
  #   super$endPoint = "/exp-site/getAll?id="
  # ),
  
  public = list(
    
    initialize = function(user=NULL, password=NULL, authentication=NULL, token=NULL, user_agent=NULL,
                          serverURL, version ){ #, endPoint) {
      super$initialize(user, password, authentication, token, user_agent, serverURL, version)#, endPoint)
    },
    
    #ag_get_phenomea_studyId = function(studyDbId, format, ...){},
    ag_get_manprac_sitecropId = function(siteCropDbId, format, ...){} ,
    ag_get_manprac_expsiteId = function(expsiteDbId, format, ...){}
    
  )
)

#############################################

#' @title  Get all Management measurements based on the experiment site ID
#' @description retrieve Management measurements data from AGROFIMS database. AGROFIMS use the AgAPI standard in order to get and post data.
#' @field ... argument inherents by AgaAPIClient
#' @field siteCropDbId character siteCropId its the id of the Management evaluated in one site and experiment
#' @field format support in three data structures: json, list and data.frames
#' @importFrom R6 R6Class
#' @importFrom httr content
#' @importFrom jsonlite fromJSON
#' @importFrom tibble rownames_to_column
#' @author Omar Benites
#' @export 
#' 
AgManPrac$set(which = "public", name = "ag_get_manprac_sitecropId", 
               function( siteCropDbId =NULL,
                         format=c("json","list","data.frame"),
                         ... ){  
                 
                 super$endPoint <- "/crop_man_practices/getAll?id="
                 url  <- paste0(self$serverURL, self$version, super$endPoint) #everything before the URL
                 print(url)
                 
                 #GET parameters for retrieving data ----------------------------
                 #headerParams <- character()
                 queryParams <- list(id = siteCropDbId)  
                 
                 #Iterate over exp_site_id to extract experiment descript from each site in the study
                 
                 res <- self$call_api(
                   url = url, 
                   method = "GET",
                   queryParams = queryParams, #, #TODO
                   #headerParams = headerParams, #TODO
                   #body = body,
                   ...
                 )    
                 cont <- httr::content(res, as = "text", encoding = "UTF-8")
                 #Object structure
                 if(format=="json"){
                   out <-  cont
                 } else if(format=="list"){
                   out <- jsonlite::fromJSON(cont,simplifyVector = "vector")
                 } else if(format=="data.frame") {
                   out <- ragapi::as_data_frame_agapi(cont)
                 }
                 
                 return(out)
                 
               },
               
               overwrite = TRUE)   


##TODO: agregar un metodo para sacar los measurementes de un sitio-fieldbook


#############################################

#' @title  Get all Management measurements based on the agronomic experiment site database ID
#' @description retrieve Management measurements data from AGROFIMS database with AgAPI standard
#' @field ... argument inherents by AgaAPIClient
#' @field expsiteDbId character agronomical study id
#' @field format support in three data structures: json, list and data.frames
#' @importFrom R6 R6Class
#' @importFrom httr content
#' @importFrom jsonlite fromJSON
#' @importFrom tibble rownames_to_column
#' @author Omar Benites
#' @examples \dontrun{
#' library(ragapi)
#' .x <- AgManPrac$new(serverURL="https://research.cip.cgiar.org/agrofims/api/dev", version="/0253/r")
#' out <- .x$ag_get_manprac_expsiteId(expsiteDbId= 11, format="data.frame")
#' }
#' @export 
#' 
AgManPrac$set(which = "public", name = "ag_get_manprac_expsiteId", 
               function(expsiteDbId =NULL,
                        format=c("json","list","data.frame"),
                        ... ){  
                 
                 super$endPoint <- "/crop_man_practices/getAll?id="
                 url  <- paste0(self$serverURL, self$version, super$endPoint) #everything before the URL
                 
                 headerParams <- character()
                 
                 queryParams <- list(id = expsiteDbId) #everythig after the ? in the URL 
                 
                 res <- self$call_api(
                   url = url, 
                   method = "GET",
                   queryParams = queryParams, #, #TODO
                   #headerParams = headerParams, #TODO
                   #body = body,
                   ...
                 )
                 cont <- httr::content(res, as = "text", encoding = "UTF-8")
                 
                 if(format=="json"){
                   out <-  cont
                 } else if(format=="list"){
                   out <- jsonlite::prettify(txt = cont) #jsonlite::fromJSON(cont)
                 } else if(format=="data.frame") {
                   out <- as_data_frame_agapi(cont)
                   #cont <- jsonlite::fromJSON(cont)
                   #out <- replace_null(cont,"") %>% as.data.frame(stringsAsFactors=FALSE) %>% tibble::rownames_to_column()
                 }
                 return(out)
                 
                 # #Create objet AgExpSite -------------------------------------------
                 # obj_expsite <- AgExpSite$new(serverURL = self$serverURL ,
                 #                              version = self$version )
                 # print(obj_expsite)
                 # #Get experiment sites studies -------------------------------
                 # dt_expsite <- obj_expsite$ag_get_cropsite_expsiteId(expsiteDbId= expsiteDbId, format="data.frame")
                 # sitecrop_id <- dt_expsite$siteCropId
                 # print(sitecrop_id)
                 # 
                 # super$endPoint <- "/crop-Management/getAll?id="
                 # url  <- paste0(self$serverURL, self$version, super$endPoint) #everything before the URL
                 # print(url)
                 # 
                 # #GET parameters for retrieving data ----------------------------
                 # #headerParams <- character()
                 # queryParams <- vector(mode="list",length = 1)
                 # 
                 # #Allocate response objects from GET method ----------------------
                 # res <- out <-  vector(mode="list", length = length(sitecrop_id))
                 # 
                 # #Iterate over exp_site_id to extract Management information by site from each site in the study
                 # for(i in 1:length(sitecrop_id)){
                 #   queryParams <- list(id = sitecrop_id[i])  
                 #   res[[i]] <- self$call_api(
                 #     url = url, 
                 #     method = "GET",
                 #     queryParams = queryParams, #, #TODO
                 #     #headerParams = headerParams, #TODO
                 #     #body = body,
                 #     ...
                 #   )    
                 #   cont <- httr::content(res[[i]], as = "text", encoding = "UTF-8")
                 #   #Object structure
                 #   if(format=="json"){
                 #     out[[i]] <-  cont
                 #   } else if(format=="list"){
                 #     out[[i]] <- jsonlite::fromJSON(cont,simplifyVector = "vector")
                 #   } else if(format=="data.frame") {
                 #     out[[i]] <- as_data_frame_agapi(cont)
                 #   }
                 # }
                 # return(out)
                 
               },
overwrite = TRUE
)