Added dataset download rule

.gitignore

@@ -87,3 +87,9 @@ target/
 
 # Mypy cache
 .mypy_cache/
+.Rprofile
+packrat/lib*/
+packrat/*
+!packrat/packrat.lock
+!packrat/packrat.opts
+.snakemake/

Snakefile

@@ -0,0 +1,29 @@
+configfile: "config.yaml"
+include: "rules/preprocessing.snakefile"
+
+rule all:
+    input:
+        expand("data/raw/{pid}/{sensor}.csv", pid=config["PIDS"], sensor=config["SENSORS"])
+
+# --- Packrat Rules --- #
+## Taken from https://github.com/lachlandeer/snakemake-econ-r
+
+## packrat_install: installs packrat onto machine
+rule packrat_install:
+    shell:
+        "R -e 'install.packages(\"packrat\", repos=\"http://cran.us.r-project.org\")'"
+
+## packrat_install: initialize a packrat environment for this project
+rule packrat_init:
+    shell:
+        "R -e 'packrat::init()'"
+
+## packrat_snap   : Look for new R packages in files & archives them
+rule packrat_snap:
+    shell:
+        "R -e 'packrat::snapshot()'"
+
+## packrat_restore: Installs archived packages onto a new machine
+rule packrat_restore:
+    shell:
+        "R -e 'packrat::restore()'"

config.yaml

@@ -0,0 +1,7 @@
+# Valid database table names
+SENSORS: [messages]
+
+# Participants to include in the analysis
+# You must create a file for each participant
+# named pXXX containing their device_id
+PIDS: [p01, p02]

packrat/packrat.lock

@@ -0,0 +1,155 @@
+PackratFormat: 1.4
+PackratVersion: 0.5.0
+RVersion: 3.6.1
+Repos: CRAN=https://cran.rstudio.com/
+
+Package: BH
+Source: CRAN
+Version: 1.69.0-1
+Hash: 15f597ed227897f4f793b6161260f4b9
+
+Package: DBI
+Source: CRAN
+Version: 1.0.0
+Hash: 6abedd7919c4457604c0aa44529a6683
+
+Package: R6
+Source: CRAN
+Version: 2.4.0
+Hash: 948a547c484e5bea15eee76cc53cce3f
+
+Package: RMySQL
+Source: CRAN
+Version: 0.10.17
+Hash: 095e258676be1decbe4ee1bf3c164284
+Requires: DBI
+
+Package: Rcpp
+Source: CRAN
+Version: 1.0.2
+Hash: d04e441a8d398e3d3a71f294c07fa94d
+
+Package: assertthat
+Source: CRAN
+Version: 0.2.1
+Hash: 622be49032fe50bd42e96aaef613e209
+
+Package: backports
+Source: CRAN
+Version: 1.1.5
+Hash: 35ad64fcf2063e2a52031b0f1a59d8f0
+
+Package: cli
+Source: CRAN
+Version: 1.1.0
+Hash: bc4e54014c2049f2605ad0c3ba0cce6b
+Requires: assertthat, crayon
+
+Package: crayon
+Source: CRAN
+Version: 1.3.4
+Hash: ff2840dd9b0d563fc80377a5a45510cd
+
+Package: digest
+Source: CRAN
+Version: 0.6.22
+Hash: 824be063463b3709782ef29a3e8d7079
+
+Package: dplyr
+Source: CRAN
+Version: 0.8.3
+Hash: 201287c2b23cff8b2ef156ec8b1e57f2
+Requires: BH, R6, Rcpp, assertthat, glue, magrittr, pkgconfig, plogr,
+    rlang, tibble, tidyselect
+
+Package: ellipsis
+Source: CRAN
+Version: 0.3.0
+Hash: 30b58109e4d7c6184a9c2e32f9ae38c6
+Requires: rlang
+
+Package: fansi
+Source: CRAN
+Version: 0.4.0
+Hash: f147621f72b561485bfffcae78c4f5d5
+
+Package: glue
+Source: CRAN
+Version: 1.3.1
+Hash: 660bbbe3803c7cf7c9489a7d99a9c0ed
+
+Package: magrittr
+Source: CRAN
+Version: 1.5
+Hash: bdc4d48c3135e8f3b399536ddf160df4
+
+Package: packrat
+Source: CRAN
+Version: 0.5.0
+Hash: 498643e765d1442ba7b1160a1df3abf9
+
+Package: pillar
+Source: CRAN
+Version: 1.4.2
+Hash: 28ff1862b4e0c8761efca442e80a63d8
+Requires: cli, crayon, fansi, rlang, utf8, vctrs
+
+Package: pkgconfig
+Source: CRAN
+Version: 2.0.3
+Hash: 5ff5f2361851a49534c96caa2a8071c7
+
+Package: plogr
+Source: CRAN
+Version: 0.2.0
+Hash: 81a8008a5e7858552503935f1abe48aa
+
+Package: purrr
+Source: CRAN
+Version: 0.3.3
+Hash: d4f497f8a97ef6c7182a87b2476748d1
+Requires: magrittr, rlang
+
+Package: rlang
+Source: CRAN
+Version: 0.4.0
+Hash: eabda67321fe1d477ea641ddd5d84f00
+
+Package: stringi
+Source: CRAN
+Version: 1.4.3
+Hash: ed2a82fc7cc668c1345223d938cdfaf2
+
+Package: stringr
+Source: CRAN
+Version: 1.4.0
+Hash: 67da32dbb2a7a16f2ef124336358e54a
+Requires: glue, magrittr, stringi
+
+Package: tibble
+Source: CRAN
+Version: 2.1.3
+Hash: f59680d81ddc45fa3fcb8c07686d1d89
+Requires: cli, crayon, fansi, pillar, pkgconfig, rlang
+
+Package: tidyselect
+Source: CRAN
+Version: 0.2.5
+Hash: 9ab4ed03f4b7bbdbd1db9d7a920aae1a
+Requires: Rcpp, glue, purrr, rlang
+
+Package: utf8
+Source: CRAN
+Version: 1.1.4
+Hash: f3f97ce59092abc8ed3fd098a59e236c
+
+Package: vctrs
+Source: CRAN
+Version: 0.2.0
+Hash: daf77cb3dbcacd7fb619cb3748dc215f
+Requires: backports, digest, ellipsis, glue, rlang, zeallot
+
+Package: zeallot
+Source: CRAN
+Version: 0.1.0
+Hash: 10b2ed48e202b4db421ae864041dc4b2

packrat/packrat.opts

@@ -0,0 +1,19 @@
+auto.snapshot: FALSE
+use.cache: FALSE
+print.banner.on.startup: auto
+vcs.ignore.lib: TRUE
+vcs.ignore.src: FALSE
+external.packages: 
+local.repos: 
+load.external.packages.on.startup: TRUE
+ignored.packages: 
+ignored.directories:
+    data
+    inst
+quiet.package.installation: TRUE
+snapshot.recommended.packages: FALSE
+snapshot.fields:
+    Imports
+    Depends
+    LinkingTo
+symlink.system.packages: TRUE

rules/preprocessing.snakefile

@@ -0,0 +1,9 @@
+rule download_dataset:
+    input:
+        "data/external/{pid}"
+    params:
+        group="AAPECS"
+    output:
+        "data/raw/{pid}/{sensor}.csv"
+    script:
+        "../src/data/download_dataset.R"

src/data/download_dataset.R

@@ -0,0 +1,24 @@
+if (exists("snakemake"))
+    source("packrat/init.R")
+
+library(RMySQL)
+library(stringr)
+library(dplyr)
+
+participant <- snakemake@input[[1]]
+group <- snakemake@params[[1]]
+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 = "")
+sensor_data <- dbGetQuery(stopDB, query)
+sensor_data <- sensor_data[order(sensor_data$timestamp),]
+
+# Droping duplicates on all columns except for _id
+sensor_data <- sensor_data %>% distinct(!!!syms(setdiff(names(sensor_data), "_id")))
+write.table(sensor_data, sensor_file, row.names = FALSE, quote = FALSE, sep = ",")
+dbDisconnect(stopDB)