Add readable time script

Snakefile

@@ -3,7 +3,8 @@ include: "rules/preprocessing.snakefile"
 
 rule all:
     input:
-        expand("data/raw/{pid}/{sensor}.csv", pid=config["PIDS"], sensor=config["SENSORS"])
+        expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
+        expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SENSORS"])
 
 # --- Packrat Rules --- #
 ## Taken from https://github.com/lachlandeer/snakemake-econ-r

packrat/packrat.lock

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rules/preprocessing.snakefile

@@ -2,8 +2,20 @@ rule download_dataset:
     input:
         "data/external/{pid}"
     params:
-        group="AAPECS"
+        group = "AAPECS",
+        table = "{sensor}"
     output:
-        "data/raw/{pid}/{sensor}.csv"
+        "data/raw/{pid}/{sensor}_raw.csv"
     script:
-        "../src/data/download_dataset.R"
+        "../src/data/download_dataset.R"
+
+rule readable_datetime:
+    input:
+        sensor_input = rules.download_dataset.output
+    params:
+        timezones = None,
+        fixed_timezone = "EST"
+    output:
+        "data/raw/{pid}/{sensor}_with_datetime.csv"
+    script:
+        "../src/data/readable_datetime.R"

src/data/download_dataset.R

@@ -1,20 +1,19 @@
-if (exists("snakemake"))
+source("packrat/init.R")
-    source("packrat/init.R")
 
 library(RMySQL)
 library(stringr)
 library(dplyr)
 
 participant <- snakemake@input[[1]]
-group <- snakemake@params[[1]]
+group <- snakemake@params[["group"]]
+table <- snakemake@params[["table"]]
 sensor_file <- snakemake@output[[1]]
 
 device_id <- readLines(participant, n=1)
 rmysql.settingsfile <- "./.env"
-sensor <- tools::file_path_sans_ext(basename(sensor_file))
 
 stopDB <- dbConnect(MySQL(), default.file = rmysql.settingsfile, group = group)
-query <- paste("SELECT * FROM ", sensor, " WHERE device_id LIKE '", device_id, "'", sep = "")
+query <- paste("SELECT * FROM ", table, " WHERE device_id LIKE '", device_id, "'", sep = "")
 sensor_data <- dbGetQuery(stopDB, query)
 sensor_data <- sensor_data[order(sensor_data$timestamp),]
 

src/data/readable_datetime.R

@@ -0,0 +1,43 @@
+source("packrat/init.R")
+
+library("tidyverse")
+
+input <- read.csv(snakemake@input[[1]])
+sensor_output <- snakemake@output[[1]]
+timezone_periods <- snakemake@params[["timezone_periods"]]
+fixed_timezone <- snakemake@params[["fixed_timezone"]]
+
+if(!is.null(timezone_periods)){
+    timezones <- read.csv(timezones)
+    tz_starts <- timezones$start
+    output <- input %>% 
+                mutate(timezone = findInterval(timestamp / 1000, tz_starts), # Set an interval ID based on timezones' start column
+                        timezone = ifelse(timezone == 0, 1, timezone), # Correct the first timezone ID
+                        timezone = recode(timezone, !!! timezones$timezone), # Swap IDs for text labels
+                        timezone = as.character(timezone)) %>%
+                rowwise() %>%
+                mutate(utc_date_time = as.POSIXct(timestamp/1000, origin="1970-01-01", tz="UTC"),
+                        local_date_time = format(utc_date_time, tz = timezone, usetz = F),
+                        local_date = as.Date(local_date_time),
+                        local_time = strsplit(local_date_time, " ")[[1]][2],
+                        local_hour = as.numeric(strsplit(local_time, ":")[[1]][1]),
+                        day_segment = case_when(local_hour %in% 0:5 ~ "night",
+                                                local_hour %in% 6:11 ~ "morning",
+                                                local_hour %in% 12:17 ~ "afternoon",
+                                                local_hour %in% 18:23 ~ "evening"))
+
+    write.csv(output, sensor_output)
+} else if(!is.null(fixed_timezone)){
+    output <- input %>% 
+                mutate(utc_date_time = as.POSIXct(timestamp/1000, origin="1970-01-01", tz="UTC"),
+                        local_date_time = format(utc_date_time, tz = fixed_timezone, usetz = F),
+                        local_date = as.Date(local_date_time),
+                        local_time = strsplit(local_date_time, " ")[[1]][2],
+                        local_hour = as.numeric(strsplit(local_time, ":")[[1]][1]),
+                        local_day_segment = case_when(local_hour %in% 0:5 ~ "night",
+                                                local_hour %in% 6:11 ~ "morning",
+                                                local_hour %in% 12:17 ~ "afternoon",
+                                                local_hour %in% 18:23 ~ "evening"))
+
+    write.csv(output, sensor_output)
+}