rapids/src/data/create_participants_files.R

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source("renv/activate.R")
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#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
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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$CSV_FILE_PATH, col_types=cols_only(device_id="c",pid="c",label="c",platform="c",
start_date=col_datetime(),end_date=col_datetime(),fitbit_id="c",empatica_id="c")) %>%
mutate(start_date = as.character(start_date), end_date = as.character(end_date)) # we read as date to validate format
participants <- participants %>%
mutate(!!phone_device_id_column := str_replace_all(!!rlang::sym(phone_device_id_column), ";",","),
!!fitbit_device_id_column := str_replace_all(!!rlang::sym(fitbit_device_id_column), ";",","),
!!empatica_device_id_column := str_replace_all(!!rlang::sym(empatica_device_id_column), ";",","),
platform = str_replace_all(platform, ";",","),
!!phone_device_id_column := if_else(!!rlang::sym(phone_device_id_column) %in% phone_ignored, NA_character_, !!rlang::sym(phone_device_id_column)),
!!empatica_device_id_column := if_else(!!rlang::sym(empatica_device_id_column) %in% empatica_ignored, NA_character_, !!rlang::sym(empatica_device_id_column)),
!!fitbit_device_id_column := if_else(!!rlang::sym(fitbit_device_id_column) %in% fitbit_ignored, NA_character_, !!rlang::sym(fitbit_device_id_column)))
dir.create(file.path("./data/external/participant_files/"))
participants %>%
pwalk(function(add_phone_section, add_fitbit_section, phone_device_id_column, fitbit_device_id_column, ...) {
empty_phone <- c("PHONE:", " DEVICE_IDS:", " PLATFORMS:"," LABEL:", " START_DATE:", " END_DATE:")
empty_fitbit <- c("FITBIT:", " DEVICE_IDS:", " LABEL:", " START_DATE:", " END_DATE:")
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empty_empatica <- c("EMPATICA:", " LABEL:", " START_DATE:", " END_DATE:")
row <- tibble(...)
lines <- c()
start_date = if_else(is.na(row$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)
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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],"]"),
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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")