valid_variables_script2.R

rm(list=ls())

dir_name <- readline("Introduce the name of the directory please: ")
#/Users/gnl/Documents/CTB UPM/UNCOVER/uncover_harmonization
#C:/Users/guill/Documents/harmonize_scripts

setwd(dir_name)

source("dependency_installer.R")
source("connection_parameters.R")
source("necessary_functions_connection.R")
#source("required_folder_checker.R")
#source("argument_hasher.R")


dep_list = c("jsonlite", "stringr","DSI","DSOpal","DSLite", "fields", "metafor", "ggplot2", "gridExtra", "data.table", "dsBaseClient", "openxlsx")
install_dependencies(dep_list)

codebook_file <- "20220315_Data_Harmonisation.xlsb.xlsx"

codebook_demo <- read.xlsx(codebook_file , sheet = 2 )
codebook_com_and_rf <- read.xlsx(codebook_file , sheet = 3 ) 

codebook_home_med <- read.xlsx(codebook_file , sheet = 4 ) 
codebook_si_sympt <- read.xlsx(codebook_file , sheet = 5 ) 

codebook_treatments <- read.xlsx(codebook_file , sheet = 6 ) 
codebook_labo <- read.xlsx(codebook_file , sheet = 7 ) 

codebook_complications <- read.xlsx(codebook_file , sheet = 8 ) 
codebook_imaging_data <- read.xlsx(codebook_file , sheet = 9 ) 

codebook_lifestyle_diet <- read.xlsx(codebook_file , sheet = 10 ) 
codebook_dates <- read.xlsx(codebook_file , sheet = 11 )

codebook <- rbind(codebook_demo , codebook_com_and_rf)
codebook <- rbind(codebook , codebook_home_med)
codebook <- rbind(codebook , codebook_si_sympt)
codebook <- rbind(codebook , codebook_treatments)
codebook <- rbind(codebook , codebook_labo)
codebook <- rbind(codebook , codebook_complications)
codebook <- rbind(codebook , codebook_imaging_data)

codebook_lifestyle_diet <- codebook_lifestyle_diet[, !names(codebook_lifestyle_diet) %in% c("X2", "X4" , "X10")] 
codebook <- rbind(codebook , codebook_lifestyle_diet)
codebook <- rbind(codebook , codebook_dates)


codebook_col_names <- as.data.frame(codebook$Harmonised.variable.name)

names(codebook_col_names) <- c("col_names")

#----------------------------------------------------------------------------

#Test if column names are valid
check_column_names <- function(codebook_param, colnames){
  
  str_res <- "The column names:"
  valid_colnames <- c()
  
  for(i in 1:(nrow(colnames))){
    colname <- colnames[i,1]
    number_of_column <- check_valid_name(colname ,  colnames) 
    if(number_of_column != 1){
      str_res<- paste(str_res, colname, sep=" ")
    }else{
      valid_colnames <- c(valid_colnames, colname)
    }
  }
  
  str_res<- paste(str_res,"are not registered in the harmonized data codebook \n", sep=" ")
  
  result <- list("not_colnames" = str_res , "colnames" = valid_colnames)
  
  return (result)
}

#Test if a single variable name is valid
check_valid_name <- function(col_name , col_names){
  
  valid <- 0
  
  if(col_name %in% codebook_col_names$col_names){
    
    valid <- length(grep(col_name, col_names))
    
  }
  
  return (valid)
  
}

remove_space <- function(x){
  searchString <- ' '
  replacementString <- ''
  res = sub(searchString,replacementString,x)
  return(res)
}

remove_spaces_from_ds <- function(ds){
  
  res<- lapply(ds,remove_space )
  
  return(as.data.frame(res))
  
}

is_number <- function(x){
  res <- FALSE
  
  
  if(length(x)!=0){
    x <- str_replace(x,",",".")
    
    aux <- as.numeric(x)
    
    
    if(!is.na(aux))
      res <- TRUE
  }
  
  
  return(res)
  
}


# A esta funcion la llamamos unicamente con las columnas que el sabemos que el nombre es correcto
# Usa codebook param. Si algún cambia el codebook agradeceremos esto.
check_values_format <- function(valid_columns, codebook_param){
  res <- ""
  variables_out_of_range = "Variables out of range:"
  for(i in 1:length(valid_columns[[1]])){
  #for(i in 1:1){
    current_column <- valid_columns[[1]][[i]]
    print(current_column)
    variable_type <- codebook_param$Variable.type[codebook$Harmonised.variable.name == current_column]
    possible_values <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == current_column]
    
    if (length(variable_type) > 1 || is.na(variable_type) || is.na(possible_values)){
      print(paste("Variable" , current_column , "skipped" ,  sep= " ")) 
      next
    }
    
    print(variable_type)
    if(variable_type == "Continuous"){
      
      ################## ESTO PODRÍA IR EN UNA FUNC DIFERENTE #############
      
      ### parse del formato de una variable continua ##
      ## esta sentencia funciona codebook$Possible.values.format[codebook$Harmonised.variable.name == "CMXDE"] pruebala en el interprete.
      value_format <- strsplit(possible_values, " / ")[[1]]
      low_limit <- str_trim(gsub(",", ".", (sub("-.*", "", value_format[1]))))
      high_limit <- str_trim(gsub(",", ".", (sub(".*-", "", value_format[1]))))
      if(low_limit == ""){
        low_limit <- str_trim(sub(",.*", "", value_format[1]))
        high_limit <- str_trim(sub(".*,", "", value_format[1]))
      }
      ### parse del formato de una variable continua ##
      
      tryCatch(
        error = function(cnd) {
          if(grepl("list them with datashield.errors()",cnd))
            error <- paste("Unable to analyse data" , datashield.errors() , sep = " ")
          else
            error <- paste("Unable to analyse data" , cnd, sep = " ")
          print(error)
          res <- c(res, error)
          variables_out_of_range <- paste(variables_out_of_range, current_column, "Unable to analyze , check just in case, the format should be:", possible_values ,sep = " ")
          variables_out_of_range <- paste(variables_out_of_range , "" , sep = "\n")
        },
        {
          print(paste("Higher Limit: ", high_limit))
          ds.dataFrameSubset(df.name = "data",
                                   V1.name = paste("data$", current_column, sep=""),
                                   V2.name = high_limit,
                                   Boolean.operator = "<=",
                                   newobj = "inRangeHigh",
                                   keep.NAs = TRUE,
                                   datasources = connections)
          
          print(paste("Lower Limit: ", low_limit))
          ds.dataFrameSubset(df.name = "inRangeHigh",
                                   V1.name = paste("inRangeHigh$", current_column, sep=""),
                                   V2.name = low_limit,
                                   Boolean.operator = ">=",
                                   newobj = "inRange",
                                   keep.NAs = TRUE,
                                   datasources = connections)
          
          summary <- ds.summary(paste("inRange$", current_column, sep=""))
          if(ds.length(paste("data$", current_column, sep=""))[[1]] > summary[[1]][[2]]){
            variables_out_of_range <- paste(variables_out_of_range, current_column, "the range should be:" , possible_values ,sep = " ")
            variables_out_of_range <- paste(variables_out_of_range , "" , sep = "\n")
            print(paste(current_column,  "does not follow the established format", sep=" "))
            print(paste("It should follow the following format: ", possible_values))
          }
          else{
            print(paste(paste("Data in: ", current_column), " was valid"))
          }
        }
      )
      ################## FIN ESTO PODRÍA IR EN UNA FUNC DIFERENTE #############
      
    }else if (variable_type == "Categorical" || variable_type == "Binary"){
      value_format <- lapply(strsplit(possible_values, "/") , str_trim)[[1]]
      tryCatch(
        error = function(cnd) {
          if(grepl("list them with datashield.errors()",cnd))
            error <- paste("Unable to analyse data" , datashield.errors() , sep = " ")
          else
            error <- paste("Unable to analyse data" , cnd, sep = " ")
          print(error)
          res <- c(res, error)
          variables_out_of_range <- paste(variables_out_of_range, current_column, "Unable to analyze , check just in case, the format should be:", possible_values ,sep = " ")
          variables_out_of_range <- paste(variables_out_of_range , "" , sep = "\n")
        },
        {
          contingency_table <- ds.table(paste("data$",current_column,sep=""))
          row_names <- rownames(contingency_table[[1]][[3]])
          result <- FALSE
          for (i in 1:length(row_names)) {
            if(row_names[i] == "NA")
              next
            if(!row_names[i] %in% value_format){
              variables_out_of_range <- paste(variables_out_of_range, current_column, "the range should be:" , possible_values ,sep = " ")
              variables_out_of_range <- paste(variables_out_of_range , "" , sep = "\n")
              print(paste(current_column,  "does not follow the established format", sep=" "))
              print(paste("It should follow the following format:", possible_values))
              print(paste("Instead of:", paste(row_names, collapse = " ")))
              result <- TRUE
              break
            }
          }
          if(!result){
            print(paste(paste("Data in: ", current_column), " was valid"))
          }
        }
      )
    }
  }
  return (variables_out_of_range)
}



auxConnections <- connect()
connections <- auxConnections[[1]]
inp <- auxConnections[[2]]

#Conexión a la base de datos

 ds.dim("data", datasources = connections)
 colnames <- ds.colnames("data")
 colnames

#----------------------------------------------------------------------------

#Check valid column names
datastructure_name <- "data"
data_colnames <- ds.colnames(x=datastructure_name, datasources= connections)

data_colnames <- as.data.frame(data_colnames)

check_valid_columns <- check_column_names(codebook ,data_colnames)
valid_columns <- as.data.frame(check_valid_columns$colnames)
res <- ""
res <- check_values_format(valid_columns, codebook)
cat(res)
cat(check_valid_columns$not_colnames)

datashield.logout(connections)