rm(list=ls()) dir_name <- readline("Introduce the name of the directory please: ") #/Users/gnl/Documents/CTB UPM/UNCOVER/uncover_harmonization 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$Harmonised.variable.name) names(codebook_col_names) <- c("col_names") categoric_vars = c("DMRGENDR", "DMRBORN", "DMRRETH1", "DMROCCU", "DMRHREDU", "DSXOS", "DSXHO", "DSXIC", "TRXAV","TRXRIB","TRXLR","TRXRM","TRXIA","TRXIB","TRXCH","TRXAB","TRXCS","TRXHEP","TRXAF","TRXCP","TRXOT","TRXECM","TRXIV","TRXNIV","TRXNO","TRXOX","TRXRR","TRXTR","TRXVA","TRXPE","TRXPV","TRXIT","TRXNMB","TRXAC","TRXINA","TRXIS","TRXIM","TRXVC","TRXVD","TRXZN", "CSXCOT","CSXCTR","SMXASAH","SMXFEA","SMXCOA","SMXSTA","SMXSBA","SMXRNA","SMXMYA","SMXARA","SMXCPA","SMXAPA","SMXINA","SMXNAA","SMXDIA","SMXFAA","SMXHEA","SMXCNA","SMXACA","SMXSLA","SMXTLA","SMXSYA","SMXWHA","SMXLYA","SMXANA","SMXIWA","SMXSRA","SMXBLA","CMXPRG","CMXCVD","CMXCMP","CMXHT","CMXDI","CMXCKD","CMXCLD","CMXCPD","CMXASM","CMXCND","CMXRHE","CMXCCI","CMXCBD","CMXDE","CMXPU","CMXST","CMXLY","CMXAP","RFXSM","RFXFSM","RFXOB","RFXTB","RFXIMD","RFXHIV","RFXAIDS","RFXUI","RFXHC","RFXONC","RFXMN", "HMRACI","HMRARB","HMRAHO","HMRNS","HMROS","HMRCS","HMRIS","HMRAV","HMRAB","HMRCOV","IMDXCT","IMDXCTCR","IMDXCTTE","IMDXCTAB","IMDXXR","IMDXPN", "COXRD","COXAR","COXPM","COXMOD","COXPT","COXEC","COXSH","COXIO","COXPE","COXST","COXDIC","COXRIO","COXKF","COXHF","COXBC") #---------------------------------------------------------------------------- #Test if column names are valid check_column_names <- function(codebook_param, colnames){ str_res <- "The column names:" valid_colnames <- c() for(i in 1:(nrow(colnames))){ colname <- colnames[i,1] number_of_column <- check_valid_name(colname , colnames) if(number_of_column != 1){ str_res<- paste(str_res, colname, sep=" ") }else{ valid_colnames <- c(valid_colnames, colname) } } str_res<- paste(str_res,"are not registered in the harmonized data codebook \n", sep=" ") result <- list("not_colnames" = str_res , "colnames" = valid_colnames) return (result) } #Test if a single variable name is valid check_valid_name <- function(col_name , col_names){ valid <- 0 if(col_name %in% codebook_col_names$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) } check_values_format <- function(valid_columns){ res <- "" for(i in 1:length(valid_columns[[1]])){ print(i) current_column <- valid_columns[[1]][[i]] if(current_column %in% codebook_labo$Harmonised.variable.name){ index <- which(current_column, codebook_labo$Harmonised.variable.name) value_format <- strsplit(codebook_si_sympt$Possible.values.format[2], " / ")[[1]] high_limit <- as.numeric(sub("-.*", "", value_format[1])) low_limit <- as.numeric(sub(".*-", "", value_format[1])) if(codebook_labo$Variable.type[index] == "Continuous"){ ds.dataFrameSubset(df.name = "data", V1.name = paste("data$", current_column, sep=""), V2.name = high_limit, Boolean.operator = "<=", newobj = "inRangeHigh", keep.NAs = TRUE, datasources = connections) ds.dataFrameSubset(df.name = "inRangeHigh", V1.name = paste("inRangeHigh$", 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="")) > summary[[1]][[2]]){ res <- c(res, paste(current_column, "does not follow the established format" , sep="\n")) } } } } return (res) } auxConnections <- connect() connections <- auxConnections[[1]] inp <- auxConnections[[2]] #Conexión a la base de datos ds.dim("data", datasources = connections) colnames <- ds.colnames("data") colnames # ds.dataFrameSubset(df.name = "data", # V1.name = "data$LBXAPTTA", # V2.name = "130", # Boolean.operator = "<=", # newobj = "inRangeHigh", # keep.NAs = TRUE, # datasources = connections) # # lengthHigh <- ds.length(x='inRangeHigh$LBXAPTTA', datasources = connections) # # # ds.dataFrameSubset(df.name = "inRangeHigh", # V1.name = "inRangeHigh$LBXAPTTA", # V2.name = "11", # Boolean.operator = ">=", # newobj = "inRange", # keep.NAs = TRUE, # datasources = connections) # # lengthBuenos <- ds.length(x='inRange$LBXAPTTA', datasources = connections) # # summary <- ds.summary("inRange$LBXAPTTA") #---------------------------------------------------------------------------- #Check valid column names datastructure_name <- "data" data_colnames <- ds.colnames(x=datastructure_name, datasources= connections) data_colnames <- as.data.frame(data_colnames) check_valid_columns <- check_column_names(codebook ,data_colnames) valid_columns <- as.data.frame(check_valid_columns$colnames) res <- "" res <- check_values_format(valid_columns) print(res)