First working script

valid_variables_script2.R

@@ -49,9 +49,6 @@ codebook_col_names <- as.data.frame(codebook$Harmonised.variable.name)
 
 names(codebook_col_names) <- c("col_names")
 
-categoric_vars = c("DMRGENDR", "DMRBORN", "DMRRETH1", "DMROCCU", "DMRHREDU", "DSXOS", "DSXHO", "DSXIC", "TRXAV","TRXRIB","TRXLR","TRXRM","TRXIA","TRXIB","TRXCH","TRXAB","TRXCS","TRXHEP","TRXAF","TRXCP","TRXOT","TRXECM","TRXIV","TRXNIV","TRXNO","TRXOX","TRXRR","TRXTR","TRXVA","TRXPE","TRXPV","TRXIT","TRXNMB","TRXAC","TRXINA","TRXIS","TRXIM","TRXVC","TRXVD","TRXZN",                         "CSXCOT","CSXCTR","SMXASAH","SMXFEA","SMXCOA","SMXSTA","SMXSBA","SMXRNA","SMXMYA","SMXARA","SMXCPA","SMXAPA","SMXINA","SMXNAA","SMXDIA","SMXFAA","SMXHEA","SMXCNA","SMXACA","SMXSLA","SMXTLA","SMXSYA","SMXWHA","SMXLYA","SMXANA","SMXIWA","SMXSRA","SMXBLA","CMXPRG","CMXCVD","CMXCMP","CMXHT","CMXDI","CMXCKD","CMXCLD","CMXCPD","CMXASM","CMXCND","CMXRHE","CMXCCI","CMXCBD","CMXDE","CMXPU","CMXST","CMXLY","CMXAP","RFXSM","RFXFSM","RFXOB","RFXTB","RFXIMD","RFXHIV","RFXAIDS","RFXUI","RFXHC","RFXONC","RFXMN",                         "HMRACI","HMRARB","HMRAHO","HMRNS","HMROS","HMRCS","HMRIS","HMRAV","HMRAB","HMRCOV","IMDXCT","IMDXCTCR","IMDXCTTE","IMDXCTAB","IMDXXR","IMDXPN",                         "COXRD","COXAR","COXPM","COXMOD","COXPT","COXEC","COXSH","COXIO","COXPE","COXST","COXDIC","COXRIO","COXKF","COXHF","COXBC")
-
-
 #----------------------------------------------------------------------------
 
 #Test if column names are valid
@@ -132,8 +129,8 @@ is_number <- function(x){
 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 1:9){
+  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]
@@ -150,12 +147,13 @@ check_values_format <- function(valid_columns, codebook_param){
       
       ### 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(codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == current_column], " / ")[[1]]
-      high_limit <- str_trim(gsub(",", ".", (sub("-.*", "", value_format[1]))))
-      low_limit <- str_trim(gsub(",", ".", (sub(".*-", "", value_format[1]))))
+      possible_values <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == current_column]
+      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 == ""){
-        high_limit <- str_trim(sub(",.*", "", value_format[1]))
-        low_limit <- str_trim(strtrimsub(".*,", "", value_format[1]))
+        low_limit <- str_trim(sub(",.*", "", value_format[1]))
+        high_limit <- str_trim(strtrimsub(".*,", "", value_format[1]))
       }
       ### parse del formato de una variable continua ##
       
@@ -169,6 +167,7 @@ check_values_format <- function(valid_columns, codebook_param){
           res <- c(res, error)
         },
         {
+          print(paste("Higher Limit: ", high_limit))
           ds.dataFrameSubset(df.name = "data",
                                    V1.name = paste("data$", current_column, sep=""),
                                    V2.name = high_limit,
@@ -177,7 +176,7 @@ check_values_format <- function(valid_columns, codebook_param){
                                    keep.NAs = TRUE,
                                    datasources = connections)
           
-          
+          print(paste("Lower Limit: ", low_limit))
           ds.dataFrameSubset(df.name = "inRangeHigh",
                                    V1.name = paste("inRangeHigh$", current_column, sep=""),
                                    V2.name = low_limit,
@@ -190,13 +189,18 @@ check_values_format <- function(valid_columns, codebook_param){
           if(ds.length(paste("data$", current_column, sep=""))[[1]] > summary[[1]][[2]]){
             variables_out_of_range <- paste(variables_out_of_range, current_column, sep = " ")
             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(mierda, "/") , str_trim)[[1]]
+      possible_values <- codebook_param$Possible.values.format[codebook_param$Harmonised.variable.name == current_column]
+      value_format <- lapply(strsplit(possible_values, "/") , str_trim)[[1]]
       tryCatch(
         error = function(cnd) {
           if(grepl("list them with datashield.errors()",cnd))
@@ -209,14 +213,22 @@ check_values_format <- function(valid_columns, codebook_param){
         {
           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, sep = " ")
               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"))
+          }
         }
       )
     }
@@ -232,28 +244,28 @@ inp <- auxConnections[[2]]
 
 #Conexión a la base de datos
 
- # ds.dim("data", datasources = connections)
- # colnames <- ds.colnames("data")
- # colnames
- # 
+ ds.dim("data", datasources = connections)
+ colnames <- ds.colnames("data")
+ colnames
+
  # ds.dataFrameSubset(df.name = "data",
- #                    V1.name = "data$DMXBMI",
- #                    V2.name = "130",
+ #                    V1.name = "data$DMRAGEYR",
+ #                    V2.name = "150",
  #                    Boolean.operator = "<=",
  #                    newobj = "inRangeHigh",
  #                    keep.NAs = TRUE,
  #                    datasources = connections)
  # 
  # ds.dataFrameSubset(df.name = "inRangeHigh",
- #                    V1.name = "inRangeHigh$DMXBMI",
- #                    V2.name = "11",
+ #                    V1.name = "inRangeHigh$DMRAGEYR",
+ #                    V2.name = "0",
  #                    Boolean.operator = ">=",
  #                    newobj = "inRange",
  #                    keep.NAs = TRUE,
  #                    datasources = connections)
  # 
- # summary <- ds.summary("inRange$DMXBMI")
- # if(ds.length("data$DMXBMI")[[1]] > summary[[1]][[2]]){
+ # summary <- ds.summary("inRange$DMRAGEYR")
+ # if(ds.length("data$DMRAGEYR")[[1]] > summary[[1]][[2]]){
  #   res <- c(res, paste(current_column,  "does not follow the established format" , sep="\n"))
  # }