rapids/src/data/download_dataset.R

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)