48 lines
2.6 KiB
R
48 lines
2.6 KiB
R
# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
|
|
library(RMariaDB)
|
|
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 = ",")))
|
|
dbEngine <- dbConnect(MariaDB(), db = credentials[[group]][["database"]],
|
|
username = credentials[[group]][["user"]],
|
|
password = credentials[[group]][["password"]],
|
|
host = credentials[[group]][["host"]],
|
|
port = credentials[[group]][["port"]])
|
|
return(dbEngine)
|
|
}
|
|
|
|
#' @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 FITBIT_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)
|
|
}
|
|
|