source("renv/activate.R") library(RMySQL) library(stringr) library(dplyr) library(readr) participant <- snakemake@input[[1]] group <- snakemake@params[["group"]] table <- snakemake@params[["table"]] timezone <- snakemake@params[["timezone"]] sensor_file <- snakemake@output[[1]] device_ids <- readLines(participant, n=1) unified_device_id <- tail(strsplit(device_ids, ",")[[1]], 1) # Read start and end date from the participant file to filter data within that range start_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][1] end_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][2] start_datetime_utc = format(as.POSIXct(paste0(start_date, " 00:00:00"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC") end_datetime_utc = format(as.POSIXct(paste0(end_date, " 23:59:59"),format="%Y/%m/%d %H:%M:%S",origin="1970-01-01",tz=timezone), tz="UTC") stopDB <- dbConnect(MySQL(), default.file = "./.env", group = group) # Get existent columns in table query <- paste0("SELECT * FROM ", table, " LIMIT 1") available_columns <- colnames(dbGetQuery(stopDB, query)) if("device_id" %in% available_columns){ query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", gsub(",", "','", device_ids), "')") if("timestamp" %in% available_columns && !(is.na(start_datetime_utc)) && !(is.na(end_datetime_utc)) && start_datetime_utc < end_datetime_utc){ query <- paste0(query, "AND timestamp BETWEEN 1000*UNIX_TIMESTAMP('", start_datetime_utc, "') AND 1000*UNIX_TIMESTAMP('", end_datetime_utc, "')") } sensor_data <- dbGetQuery(stopDB, query) if("timestamp" %in% available_columns){ sensor_data <- sensor_data %>% arrange(timestamp) } # Unify device_id sensor_data <- sensor_data %>% mutate(device_id = unified_device_id) # Droping duplicates on all columns except for _id or id sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), c("_id", "id")))) } else { print(paste0("Table ", table, "does not have a device_id column (Aware ID) to link its data to a participant")) } write_csv(sensor_data, sensor_file) dbDisconnect(stopDB)