108 lines
5.6 KiB
R
108 lines
5.6 KiB
R
# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
|
|
library(RPostgres)
|
|
# Needs libpq-dev for compiling from source.
|
|
|
|
# Error installing package 'RPostgres':
|
|
# =====================================
|
|
#
|
|
# * installing *source* package 'RPostgres' ...
|
|
# ** package 'RPostgres' successfully unpacked and MD5 sums checked
|
|
# ** using staged installation
|
|
# Using PKG_CFLAGS=
|
|
# Using PKG_LIBS=-lpq
|
|
# Using PKG_PLOGR=
|
|
# ------------------------- ANTICONF ERROR ---------------------------
|
|
# Configuration failed because libpq was not found. Try installing:
|
|
# * deb: libpq-dev (Debian, Ubuntu, etc)
|
|
# * rpm: postgresql-devel (Fedora, EPEL)
|
|
# * rpm: postgreql8-devel, psstgresql92-devel, postgresql93-devel, or postgresql94-devel (Amazon Linux)
|
|
# * csw: postgresql_dev (Solaris)
|
|
# * brew: libpq (OSX)
|
|
# If libpq is already installed, check that either:
|
|
# (i) 'pkg-config' is in your PATH AND PKG_CONFIG_PATH contains
|
|
# a libpq.pc file; or
|
|
# (ii) 'pg_config' is in your PATH.
|
|
# If neither can detect , you can set INCLUDE_DIR
|
|
# and LIB_DIR manually via:
|
|
# R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
|
|
# --------------------------[ ERROR MESSAGE ]----------------------------
|
|
# <stdin>:1:10: fatal error: libpq-fe.h: No such file or directory
|
|
# compilation terminated.
|
|
|
|
library(yaml)
|
|
|
|
#' @description
|
|
#' Auxiliary function to parse the connection credentials from a specifc group in ./credentials.yaml
|
|
#' You can reause most of this function if you are connection to a DB or Web API.
|
|
#' It's OK to delete this function if you don't need credentials, e.g., you are pulling data from a CSV for example.
|
|
#' @param group the yaml key containing the credentials to connect to a database
|
|
#' @preturn dbEngine a database engine (connection) ready to perform queries
|
|
get_db_engine <- function(group){
|
|
# The working dir is aways RAPIDS root folder, so your credentials file is always /credentials.yaml
|
|
credentials <- read_yaml("./credentials.yaml")
|
|
if(!group %in% names(credentials))
|
|
stop(paste("The credentials group",group, "does not exist in ./credentials.yaml. The only groups that exist in that file are:", paste(names(credentials), collapse = ","), ". Did you forget to set the group in [PHONE_DATA_STREAMS][aware_mysql][DATABASE_GROUP] in config.yaml?"))
|
|
dbEngine <- dbConnect(Postgres(), db = credentials[[group]][["database"]],
|
|
user = credentials[[group]][["user"]],
|
|
password = credentials[[group]][["password"]],
|
|
host = credentials[[group]][["host"]],
|
|
port = credentials[[group]][["port"]])
|
|
return(dbEngine)
|
|
}
|
|
|
|
# This file gets executed for each PHONE_SENSOR of each participant
|
|
# If you are connecting to a database the env file containing its credentials is available at "./.env"
|
|
# If you are reading a CSV file instead of a DB table, the @param sensor_container wil contain the file path as set in config.yaml
|
|
# You are not bound to databases or files, you can query a web API or whatever data source you need.
|
|
|
|
#' @description
|
|
#' RAPIDS allows users to use the keyword "infer" (previously "multiple") to automatically infer the mobile Operative System a device was running.
|
|
#' If you have a way to infer the OS of a device ID, implement this function. For example, for AWARE data we use the "aware_device" table.
|
|
#'
|
|
#' If you don't have a way to infer the OS, call stop("Error Message") so other users know they can't use "infer" or the inference failed,
|
|
#' and they have to assign the OS manually in the participant file
|
|
#'
|
|
#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
|
|
#' @param device A device ID string
|
|
#' @return The OS the device ran, "android" or "ios"
|
|
|
|
infer_device_os <- function(stream_parameters, device){
|
|
#dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
|
|
#query <- paste0("SELECT device_id,brand FROM aware_device WHERE device_id = '", device, "'")
|
|
#message(paste0("Executing the following query to infer phone OS: ", query))
|
|
#os <- dbGetQuery(dbEngine, query)
|
|
#dbDisconnect(dbEngine)
|
|
|
|
#if(nrow(os) > 0)
|
|
# return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
|
|
#else
|
|
stop(paste("We cannot infer the OS of the following device id because the aware_device table does not exist."))
|
|
|
|
#return(os)
|
|
}
|
|
|
|
#' @description
|
|
#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
|
|
#'
|
|
#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
|
|
#' @param device A device ID string
|
|
#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
|
|
#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
|
|
#' @return A dataframe with the sensor data for device
|
|
|
|
pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
|
|
dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
|
|
query <- paste0("SELECT ", paste(columns, collapse = ",")," FROM ", sensor_container, " WHERE ", columns$DEVICE_ID ," = '", device,"'")
|
|
# Letting the user know what we are doing
|
|
message(paste0("Executing the following query to download data: ", query))
|
|
sensor_data <- dbGetQuery(dbEngine, query)
|
|
|
|
dbDisconnect(dbEngine)
|
|
|
|
if(nrow(sensor_data) == 0)
|
|
warning(paste("The device '", device,"' did not have data in ", sensor_container))
|
|
|
|
return(sensor_data)
|
|
}
|
|
|