Add readable time script
JulioV
parent
1b1799f9d8
commit
2fdf23e0af
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@ -3,7 +3,8 @@ include: "rules/preprocessing.snakefile"
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rule all:
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input:
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expand("data/raw/{pid}/{sensor}.csv", pid=config["PIDS"], sensor=config["SENSORS"])
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expand("data/raw/{pid}/{sensor}_raw.csv", pid=config["PIDS"], sensor=config["SENSORS"]),
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expand("data/raw/{pid}/{sensor}_with_datetime.csv", pid=config["PIDS"], sensor=config["SENSORS"])
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# --- Packrat Rules --- #
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## Taken from https://github.com/lachlandeer/snakemake-econ-r
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@ -18,6 +18,11 @@ Source: CRAN
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Version: 2.4.0
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Hash: 948a547c484e5bea15eee76cc53cce3f
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Package: RColorBrewer
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Source: CRAN
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Version: 1.1-2
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Hash: c0d56cd15034f395874c870141870c25
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Package: RMySQL
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Source: CRAN
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Version: 0.10.17
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@ -29,6 +34,12 @@ Source: CRAN
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Version: 1.0.2
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Hash: d04e441a8d398e3d3a71f294c07fa94d
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Package: askpass
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Source: CRAN
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Version: 1.1
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Hash: 6f6c430e3cd0dd7d48f447700f4d7e7f
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Requires: sys
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Package: assertthat
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Source: CRAN
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Version: 0.2.1
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@ -39,17 +50,63 @@ Source: CRAN
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Version: 1.1.5
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Hash: 35ad64fcf2063e2a52031b0f1a59d8f0
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Package: base64enc
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Version: 0.1-3
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Hash: c590d29e555926af053055e23ee79efb
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Version: 0.5.2
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Hash: 2c1abd749c826a39101a156ed0afc9be
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Requires: backports, dplyr, generics, purrr, reshape2, stringr, tibble,
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tidyr
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Package: callr
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Source: CRAN
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Version: 3.3.2
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Source: CRAN
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Version: 1.1.0
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Source: CRAN
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Version: 1.4.2
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tidyselect
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Package: digest
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Source: CRAN
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Version: 0.6.22
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@ -68,21 +125,146 @@ Version: 0.3.0
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Package: fs
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Source: CRAN
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Hash: 7cf3f9df0089475f133ec23befca1032
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Requires: digest, gtable, lazyeval, reshape2, rlang, scales, tibble,
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viridisLite, withr
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Package: glue
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Source: CRAN
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Version: 2.1.1
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Hash: 68fe47f9b101144fd042b7514a16313e
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Requires: Rcpp, forcats, hms, readr, tibble
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Package: highr
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Package: htmltools
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Version: 0.4.0
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Requires: Rcpp, digest, rlang
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Source: CRAN
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Version: 1.4.1
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Requires: R6, curl, jsonlite, mime, openssl
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Package: jsonlite
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Source: CRAN
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Source: CRAN
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Requires: Rcpp, stringr
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Package: magrittr
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Source: CRAN
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Requires: mime, xfun
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Package: mime
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Source: CRAN
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Version: 0.7
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Package: modelr
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Source: CRAN
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Version: 0.1.5
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Requires: broom, dplyr, magrittr, purrr, rlang, tibble, tidyr
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Package: munsell
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Source: CRAN
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Version: 0.5.0
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Package: openssl
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Package: packrat
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Source: CRAN
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Version: 0.5.0
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@ -104,17 +286,105 @@ Source: CRAN
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Hash: 81a8008a5e7858552503935f1abe48aa
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Source: CRAN
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Source: CRAN
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Source: CRAN
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Source: CRAN
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stringr, tinytex, xfun, yaml
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Package: selectr
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Source: CRAN
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Version: 1.4.3
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@ -126,18 +396,45 @@ Version: 1.4.0
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Hash: 67da32dbb2a7a16f2ef124336358e54a
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@ -149,6 +446,37 @@ Version: 0.2.0
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Source: CRAN
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Version: 0.1.0
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@ -2,8 +2,20 @@ rule download_dataset:
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input:
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"data/external/{pid}"
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params:
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group="AAPECS"
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group = "AAPECS",
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table = "{sensor}"
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output:
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"data/raw/{pid}/{sensor}.csv"
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"data/raw/{pid}/{sensor}_raw.csv"
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script:
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"../src/data/download_dataset.R"
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rule readable_datetime:
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input:
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sensor_input = rules.download_dataset.output
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params:
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timezones = None,
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fixed_timezone = "EST"
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output:
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"data/raw/{pid}/{sensor}_with_datetime.csv"
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script:
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"../src/data/readable_datetime.R"
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@ -1,4 +1,3 @@
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if (exists("snakemake"))
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source("packrat/init.R")
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library(RMySQL)
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@ -6,15 +5,15 @@ library(stringr)
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library(dplyr)
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participant <- snakemake@input[[1]]
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group <- snakemake@params[[1]]
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group <- snakemake@params[["group"]]
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table <- snakemake@params[["table"]]
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sensor_file <- snakemake@output[[1]]
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device_id <- readLines(participant, n=1)
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rmysql.settingsfile <- "./.env"
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sensor <- tools::file_path_sans_ext(basename(sensor_file))
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||||
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$timestamp),]
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,43 @@
|
|||
source("packrat/init.R")
|
||||
|
||||
library("tidyverse")
|
||||
|
||||
input <- read.csv(snakemake@input[[1]])
|
||||
sensor_output <- snakemake@output[[1]]
|
||||
timezone_periods <- snakemake@params[["timezone_periods"]]
|
||||
fixed_timezone <- snakemake@params[["fixed_timezone"]]
|
||||
|
||||
if(!is.null(timezone_periods)){
|
||||
timezones <- read.csv(timezones)
|
||||
tz_starts <- timezones$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)
|
||||
}
|
||||
Loading…
Reference in New Issue