source("renv/activate.R") #library(RMariaDB) library(stringr) library(purrr) library(readr) library("dplyr", warn.conflicts = F) config <- snakemake@params[["config"]] group <- config$SOURCE$DATABASE_GROUP timezone <- config$SOURCE$TIMEZONE phone_device_id_column = "device_id" fitbit_device_id_column = "fitbit_id" empatica_device_id_column = "empatica_id" add_phone_section = config$PHONE_SECTION$ADD add_fitbit_section = config$FITBIT_SECTION$ADD add_empatica_section = config$EMPATICA_SECTION$ADD phone_ignored = config$PHONE_SECTION$IGNORED_DEVICE_IDS fitbit_ignored = config$FITBIT_SECTION$IGNORED_DEVICE_IDS empatica_ignored = config$EMPATICA_SECTION$IGNORED_DEVICE_IDS rmysql.settingsfile <- "./.env" participants <- read_csv(config$CSV_FILE_PATH, col_types=cols_only(device_id="c",pid="c",label="c",platform="c", start_date=col_datetime(),end_date=col_datetime(),fitbit_id="c",empatica_id="c")) %>% mutate(start_date = as.character(start_date), end_date = as.character(end_date)) # we read as date to validate format participants <- participants %>% mutate(!!phone_device_id_column := str_replace_all(!!rlang::sym(phone_device_id_column), ";",","), !!fitbit_device_id_column := str_replace_all(!!rlang::sym(fitbit_device_id_column), ";",","), !!empatica_device_id_column := str_replace_all(!!rlang::sym(empatica_device_id_column), ";",","), platform = str_replace_all(platform, ";",","), !!phone_device_id_column := if_else(!!rlang::sym(phone_device_id_column) %in% phone_ignored, NA_character_, !!rlang::sym(phone_device_id_column)), !!empatica_device_id_column := if_else(!!rlang::sym(empatica_device_id_column) %in% empatica_ignored, NA_character_, !!rlang::sym(empatica_device_id_column)), !!fitbit_device_id_column := if_else(!!rlang::sym(fitbit_device_id_column) %in% fitbit_ignored, NA_character_, !!rlang::sym(fitbit_device_id_column))) dir.create(file.path("./data/external/participant_files/")) participants %>% pwalk(function(add_phone_section, add_fitbit_section, phone_device_id_column, fitbit_device_id_column, ...) { empty_phone <- c("PHONE:", " DEVICE_IDS:", " PLATFORMS:"," LABEL:", " START_DATE:", " END_DATE:") empty_fitbit <- c("FITBIT:", " DEVICE_IDS:", " LABEL:", " START_DATE:", " END_DATE:") empty_empatica <- c("EMPATICA:", " LABEL:", " START_DATE:", " END_DATE:") row <- tibble(...) lines <- c() start_date = if_else(is.na(row$start_date), "", row$start_date) end_date = if_else(is.na(row$end_date), "", row$end_date) if(add_phone_section == TRUE && !is.na(row[phone_device_id_column])){ lines <- append(lines, c("PHONE:", paste0(" DEVICE_IDS: [",row[phone_device_id_column],"]"), paste0(" PLATFORMS: [",row$platform,"]"), paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date))) }else lines <- append(lines, empty_phone) if(add_fitbit_section == TRUE && !is.na(row[fitbit_device_id_column])){ lines <- append(lines, c("FITBIT:", paste0(" DEVICE_IDS: [",row[fitbit_device_id_column],"]"), paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date))) } else lines <- append(lines, empty_fitbit) if(add_empatica_section == TRUE && !is.na(row[empatica_device_id_column])){ lines <- append(lines, c("EMPATICA:", paste0(" DEVICE_IDS: [",row[empatica_device_id_column],"]"), paste(" LABEL:",row$label), paste(" START_DATE:", start_date), paste(" END_DATE:", end_date))) } else lines <- append(lines, empty_empatica) lines <- append(lines, "\n") file_connection <- file(paste0("./data/external/participant_files/", row$pid, ".yaml")) writeLines(lines, file_connection) close(file_connection) }, add_phone_section, add_fitbit_section, phone_device_id_column, fitbit_device_id_column, empatica_device_id_column) file_lines <-readLines("./config.yaml") for (i in 1:length(file_lines)){ if(startsWith(file_lines[i], "PIDS:")){ file_lines[i] <- paste0("PIDS: ['", paste(participants$pid, collapse = "', '"), "']") } } writeLines(file_lines, con = "./config.yaml")