R/ag_soil_measurements.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
#' 
#' Soil Measurements Class
#' 
#' @description Class to represent soil measurements data from AgroFIMS. It inherents from AgAPI client class 
#' all the basic parameters and methods.
#'
#' @title AgSoilMea
#'
#' @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
#' 
AgSoilMea <- R6::R6Class(
  
  classname = "AgSoilMea",
  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_soil_studyId = function(studyDbId, format, ...){},
    ag_get_soil_expsiteId = function(expsiteDbId, format, ...){}
  )
)



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

#' @title  Get all soil measurements based on the agronomic study database ID
#' @description retrieve soil measurements data from AGROFIMS database with AgAPI standard
#' @field ... argument inherents by AgaAPIClient
#' @field studyDbID 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
#' @export 
#' 
AgSoilMea$set(which = "public", name = "ag_get_soil_studyId", 
                 function(studyDbId =NULL,
                          format=c("json","list","data.frame"),
                          ... ){  
                   
                   #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_expsite_studyId(studyDbId= studyDbId, format="data.frame")
                   expsite_id <- dt_expsite$expSiteId
                   print(expsite_id)
                   
                   super$endPoint <- "/site-soil/getAll?id="
                   url  <- paste0(self$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(expsite_id))
                   
                   #Iterate over exp_site_id to extract crop information by site from each site in the study
                   for(i in 1:length(expsite_id)){
                     queryParams <- list(id = expsite_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)   




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

#' @title  Get all soil measurements based on the experiment site ID
#' @description retrieve soil measurements data from AGROFIMS database. AGROFIMS use the AgAPI standard in order to get and post data.
#' @field ... argument inherents by AgaAPIClient
#' @field expsiteDbId character experiment site 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
#' @export 
#' 
AgSoilMea$set(which = "public", name = "ag_get_soil_expsiteId", 
                 function( expsiteDbId =NULL,
                           format=c("json","list","data.frame"),
                           ... ){  
                   
                   super$endPoint <- "/site-soil/getAll?id="
                   url  <- paste0(self$serverURL, self$version, super$endPoint) #everything before the URL
                   print(url)
                   
                   #GET parameters for retrieving data ----------------------------
                   #headerParams <- character()
                   queryParams <- list(id = expsiteDbId)  
                   
                   #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)