R/expdetails_metadata.R

In AGROFIMS/ragrofims: AgroFIMS functionalities into R

#' Replace attributes that has others values in expdetails
#'
#' @param .data data to clean up \code{Other} values
#' @param attribute attribute of the database. Attribute name from AgroFIMS database where a user input is stored 
#' @param other_attribute Other attribute name related to \code{attribute} parameter used to store \code{Other} values or non-standardized inputs. 
#' @author Omar Benites
#' @examples \dontrun{
#' .data <- ag_get_expdetails_studyId(studyDbId = 21,format = "data.frame",
#'                                    serverURL = "https://research.cip.cgiar.org/agrofims/api/dev",
#'                                    version ="/0212/r")
#' .data. <- .replace_other_attribute_expdetails(.data, "experimentType" ,"experimentTypeOther")
#' }
#' @export
#' 
.replace_other_attribute_expdetails <- function(.data, attribute, other_attribute){
    
    value <- .data[.data$DbAttribute == attribute,"Value"]
    print(value)
    #add checkers
    if(value=="Other"){
      other <- .data[.data$DbAttribute == other_attribute,"Value"]  
      .data[.data$DbAttribute == attribute,]$Value <- other
    } else if(grepl(pattern = "Other", value)) {
      other <- .data[.data$DbAttribute == other_attribute,"Value"] 
      value <- gsub(pattern = "Other", replacement = other, x = value)
      .data[.data$DbAttribute == attribute,]$Value <- value
    }  
    .data
}

#' Get other row position in expdetails data
#' 
#' @param .data data to clean up \code{Other} values
#' @param other_attribute Other attribute name related to \code{attribute} parameter used to store \code{Other} values or non-standardized inputs. 
#' @author Omar Benites
#' @examples \dontrun{
#' .data <- ag_get_expdetails_studyId(studyDbId = 21,format = "data.frame",
#'                                    serverURL = "https://research.cip.cgiar.org/agrofims/api/dev",
#'                                    version ="/0212/r")
#' .data. <- .get_other_position_expdetails(.data, "experimentTypeOther")
#' }
#' @export
#' 
.get_other_rowpos_expdetails <- function(.data, other_attribute){
    which(.data$DbAttribute==other_attribute)
}

#' Remove other values in expdtails data
#' 
#' @param .data data to clean up \code{Other} values
#' @param other_attribute Other attribute name related to \code{attribute} parameter used to store \code{Other} values or non-standardized inputs. 
#' @author Omar Benites
#' @examples \dontrun{
#' .data <- ag_get_expdetails_studyId(studyDbId = 21,format = "data.frame",
#'                                    serverURL = "https://research.cip.cgiar.org/agrofims/api/dev",
#'                                    version ="/0212/r")
#' .data. <- .remove_other_exdetails(.data, "experimentTypeOther")
#' }
#' @export
#' 
.remove_other_exdetails <- function(.data, other_attribute){
  pos <- .get_other_rowpos_expdetails(.data, other_attribute)
  .data <- .data[-pos, ] 
}

#' Clean other values in experiment details 
#' 
#' @description Tipically values users fill forms or combos with standarized inputs in AgroFIMS. However, sometimes ontologized inputs are not enough.
#' For this reason, they select the \code{Other} value in order to fill options that have not been maped in the Agronomic Ontology in AgroFIMS
#' @param .data data to clean up \code{Other} values
#' @param attribute attribute of the database. Attribute name from AgroFIMS database where a user input is stored 
#' @param other_attribute Other attribute name related to \code{attribute} parameter used to store \code{Other} values or non-standardized inputs. 
#' @author Omar Benites

#' @examples \dontrun{
#' .data <- ag_get_expdetails_studyId(studyDbId = 21,format = "data.frame",
#'                                    serverURL = "https://research.cip.cgiar.org/agrofims/api/dev",
#'                                    version ="/0212/r")
#' .data. <- clean_other_expdetails(.data, "experimentType", "experimentTypeOther")
#' }
#' 
clean_other_expdetails <- function(.data, attribute, other_attribute){
  
  .data <- .replace_other_attribute_expdetails(.data, attribute, other_attribute) 
  .data <- .remove_other_exdetails(.data, other_attribute)
  
}


###
#' Clean other values in experiment details 
#' 
#' @description Tipically values users fill forms or combos with standarized inputs in AgroFIMS. However, sometimes ontologized inputs are not enough.
#' For this reason, they select the \code{Other} value in order to fill options that have not been maped in the Agronomic Ontology in AgroFIMS
#' @param .data data to clean up \code{Other} values
#' @param attribute attribute of the database. Attribute name from AgroFIMS database where a user input is stored 
#' @param other_attribute Other attribute name related to \code{attribute} parameter used to store \code{Other} values or non-standardized inputs. 
#' @author Omar Benites
#' @export
#' @examples \dontrun{
#' .data <- ag_get_expdetails_studyId(studyDbId = 21,format = "data.frame",
#'                                    serverURL = "https://research.cip.cgiar.org/agrofims/api/dev",
#'                                    version ="/0212/r")
#' .data. <- clean_other_expdetails(.data, "experimentType", "experimentTypeOther")
#' }
#' 
clean_expdetails <- function(.data, attribute, other_attribute){
  
  #TODO: add layers to clean other columns
  .data <- clean_other_expdetails(.data, attribute, other_attribute)
  
}

###


#' Convert API-data.frame response to AgroFIMS Excel logic table
#' 
#' @param .data data.frame table with experimental details metadata
#' @param meta_dbattributes metadata attributes and labels in AgroFIMS
#' @description Transform an API table to Excel table format
#' @author Omar Benites
#' @description set and modify databases attributes by AgroFIMS label in order to export the fieldbook file
#' @export
#' 
convert_to_xlsx_expdetails <- function(.data, meta_dbattributes){
  
  out <- dplyr::left_join(.data,meta_dbattributes)
  out <- dplyr::filter(out, !is.na(AgroLabelDbAttribute))
  .data <- data.frame(Parameter = out$AgroLabelDbAttribute, 
                      Value     = out$Value, 
                      stringsAsFactors = FALSE)
}


#' Get metadata from experimental details
#' 
#' @param studyId study or experiment ID
#' @param format type of data structure format
#' @param serverURL database server URL
#' @param version api version
#' @param meta_dbattributes data dictionary of metadata. It includes equivalences between excel and database names.
#' @description get metadata from experimental details
#' @importFrom ragapi ag_get_expdetails_studyId
#' @export
#' 
get_expdetails_metadata <- function(studyId = NULL, format= NULL, 
                                    serverURL=NULL,  version = NULL,
                                    meta_dbattributes=NULL){
  

  expdetails_data <- ragapi::ag_get_expdetails_studyId(studyDbId = studyId, format = "data.frame",
                                                       serverURL = serverURL, version = version)
  
  #check if there is agronomic data under certain conditions
  cond <- nrow(expdetails_data)>1  #has_agronomic_metadata(expdetails_data)
  if(cond){
    expdetails_data <- clean_expdetails(expdetails_data, "experimenttype", "experimenttypeother")
    expdetails_data <- convert_to_xlsx_expdetails(expdetails_data, meta_dbattributes)    
  } else {
    msg <- cond
    expdetails_data<- data.frame()
  }
  
}







 
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