48 lines
2.1 KiB
R
48 lines
2.1 KiB
R
source("packrat/init.R")
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library(RMySQL)
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library(stringr)
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library(dplyr)
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participant <- snakemake@input[[1]]
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group <- snakemake@params[["group"]]
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table <- snakemake@params[["table"]]
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timezone <- snakemake@params[["timezone"]]
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sensor_file <- snakemake@output[[1]]
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device_ids <- readLines(participant, n=1)
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unified_device_id <- tail(strsplit(device_ids, ",")[[1]], 1)
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# Read start and end date from the participant file to filter data within that range
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start_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][1]
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end_date <- strsplit(readLines(participant, n=4)[4], ",")[[1]][2]
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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")
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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")
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stopDB <- dbConnect(MySQL(), default.file = "./.env", group = group)
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# Get existent columns in table
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query <- paste0("SELECT * FROM ", table, " LIMIT 1")
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available_columns <- colnames(dbGetQuery(stopDB, query))
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if("device_id" %in% available_columns){
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query <- paste0("SELECT * FROM ", table, " WHERE device_id IN ('", gsub(",", "','", device_ids), "')")
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if("timestamp" %in% available_columns && !(is.na(start_datetime_utc)) && !(is.na(end_datetime_utc)) && start_datetime_utc < end_datetime_utc){
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query <- paste0(query, "AND timestamp BETWEEN 1000*UNIX_TIMESTAMP('", start_datetime_utc, "') AND 1000*UNIX_TIMESTAMP('", end_datetime_utc, "')")
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}
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sensor_data <- dbGetQuery(stopDB, query)
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if("timestamp" %in% available_columns){
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sensor_data <- sensor_data %>% arrange(timestamp)
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}
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# Unify device_id
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sensor_data <- sensor_data %>% mutate(device_id = unified_device_id)
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# Droping duplicates on all columns except for _id or id
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sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), c("_id", "id"))))
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} else {
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print(paste0("Table ", table, "does not have a device_id column (Aware ID) to link its data to a participant"))
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}
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write.csv(sensor_data, sensor_file, row.names = FALSE)
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dbDisconnect(stopDB) |