79 lines
4.2 KiB
R
79 lines
4.2 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 = "device_id"
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fitbit_device_id_column = "fitbit_id"
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empatica_device_id_column = "empatica_id"
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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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add_empatica_section = config$EMPATICA_SECTION$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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empatica_ignored = config$EMPATICA_SECTION$IGNORED_DEVICE_IDS
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rmysql.settingsfile <- "./.env"
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participants <- read_csv(config$CSV_FILE_PATH, col_types=cols_only(device_id="c",pid="c",label="c",platform="c",
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start_date=col_datetime(),end_date=col_datetime(),fitbit_id="c",empatica_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_all(!!rlang::sym(phone_device_id_column), ";",","),
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!!fitbit_device_id_column := str_replace_all(!!rlang::sym(fitbit_device_id_column), ";",","),
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!!empatica_device_id_column := str_replace_all(!!rlang::sym(empatica_device_id_column), ";",","),
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platform = str_replace_all(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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!!empatica_device_id_column := if_else(!!rlang::sym(empatica_device_id_column) %in% empatica_ignored, NA_character_, !!rlang::sym(empatica_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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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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empty_empatica <- c("EMPATICA:", " 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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if(add_empatica_section == TRUE && !is.na(row[empatica_device_id_column])){
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lines <- append(lines, c("EMPATICA:", paste0(" DEVICE_IDS: [",row[empatica_device_id_column],"]"),
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paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date)))
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} else
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lines <- append(lines, empty_empatica)
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lines <- append(lines, "\n")
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file_connection <- file(paste0("./data/external/participant_files/", row$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, empatica_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") |