86 lines
4.7 KiB
R
86 lines
4.7 KiB
R
source("renv/activate.R")
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library(RMariaDB)
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library(stringr)
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library(purrr)
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library(readr)
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library("dplyr", warn.conflicts = F)
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config <- snakemake@params[["config"]]
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group <- config$SOURCE$DATABASE_GROUP
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timezone <- config$SOURCE$TIMEZONE
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phone_device_id_column = config$PHONE_SECTION$DEVICE_ID_COLUMN
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fitbit_device_id_column = config$FITBIT_SECTION$DEVICE_ID_COLUMN
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add_phone_section = config$PHONE_SECTION$ADD
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add_fitbit_section = config$FITBIT_SECTION$ADD
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phone_ignored = config$PHONE_SECTION$IGNORED_DEVICE_IDS
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fitbit_ignored = config$FITBIT_SECTION$IGNORED_DEVICE_IDS
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rmysql.settingsfile <- "./.env"
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if(config$SOURCE$TYPE == "AWARE_DEVICE_TABLE"){
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database <- dbConnect(MariaDB(), default.file = rmysql.settingsfile, group = group)
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if(config$FITBIT_SECTION$ADD == TRUE){
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query <- paste("SELECT",phone_device_id_column, ",",fitbit_device_id_column," as _temp_fitbit_id, brand, label, timestamp FROM aware_device order by timestamp asc")
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fitbit_device_id_column <- "_temp_fitbit_id"
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}
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else
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query <- paste("SELECT ",phone_device_id_column,", brand, label, timestamp FROM aware_device order by timestamp asc")
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participants <- dbGetQuery(database, query)
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dbDisconnect(database)
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participants <- participants %>%
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mutate(pid = if_else(row_number()<10, paste0("p","0",row_number()), paste0("p", row_number())),
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platform = if_else(brand == "iPhone", "ios", "android"), brand = NULL,
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label = iconv(if_else(label == "", "EMPTY_LABEL", label), from = "UTF-8", to = "UTF-8", sub=''),
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start_date = format(as.POSIXct(timestamp / 1000, origin = "1970-01-01", tz = timezone), "%Y-%m-%d"),
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end_date = format(Sys.Date(), "%Y-%m-%d"),
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!!phone_device_id_column := if_else(!!rlang::sym(phone_device_id_column) %in% phone_ignored, NA_character_, !!rlang::sym(phone_device_id_column)),
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!!fitbit_device_id_column := if_else(!!rlang::sym(fitbit_device_id_column) %in% fitbit_ignored, NA_character_, !!rlang::sym(fitbit_device_id_column)))
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} else if(config$SOURCE$TYPE == "CSV_FILE"){
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participants <- read_csv(config$SOURCE$CSV_FILE_PATH, col_types=cols_only(device_id="c",pid="c",label="c",platform="c",
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start_date=col_date(format = "%Y-%m-%d"),end_date=col_date(format = "%Y-%m-%d"),fitbit_id="c")) %>%
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mutate(start_date = as.character(start_date), end_date = as.character(end_date)) # we read as date to validate format
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participants <- participants %>%
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mutate(!!phone_device_id_column := str_replace(!!rlang::sym(phone_device_id_column), ";",","),
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platform = str_replace(platform, ";",","),
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!!phone_device_id_column := if_else(!!rlang::sym(phone_device_id_column) %in% phone_ignored, NA_character_, !!rlang::sym(phone_device_id_column)),
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!!fitbit_device_id_column := if_else(!!rlang::sym(fitbit_device_id_column) %in% fitbit_ignored, NA_character_, !!rlang::sym(fitbit_device_id_column)))
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}
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dir.create(file.path("./data/external/participant_files/"))
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participants %>%
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pwalk(function(add_phone_section, add_fitbit_section, phone_device_id_column, fitbit_device_id_column, ...) {
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empty_phone <- c("PHONE:", " DEVICE_IDS:", " PLATFORMS:"," LABEL:", " START_DATE:", " END_DATE:")
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empty_fitbit <- c("FITBIT:", " DEVICE_IDS:", " LABEL:", " START_DATE:", " END_DATE:")
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row <- tibble(...)
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lines <- c()
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start_date = if_else(is.na(row$start_date), "", row$start_date)
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end_date = if_else(is.na(row$end_date), "", row$end_date)
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if(add_phone_section == TRUE && !is.na(row[phone_device_id_column])){
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lines <- append(lines, c("PHONE:", paste0(" DEVICE_IDS: [",row[phone_device_id_column],"]"), paste0(" PLATFORMS: [",row$platform,"]"),
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paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date)))
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}else
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lines <- append(lines, empty_phone)
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if(add_fitbit_section == TRUE && !is.na(row[fitbit_device_id_column])){
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lines <- append(lines, c("FITBIT:", paste0(" DEVICE_IDS: [",row[fitbit_device_id_column],"]"),
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paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date)))
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} else
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lines <- append(lines, empty_fitbit)
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file_connection <- file(paste0("./data/external/participant_files/", row$pid, ".yaml"))
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writeLines(lines, file_connection)
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close(file_connection)
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}, add_phone_section, add_fitbit_section, phone_device_id_column, fitbit_device_id_column)
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file_lines <-readLines("./config.yaml")
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for (i in 1:length(file_lines)){
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if(startsWith(file_lines[i], "PIDS:")){
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file_lines[i] <- paste0("PIDS: [", paste(participants$pid, collapse = ", "), "]")
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}
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}
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writeLines(file_lines, con = "./config.yaml") |