86 lines
4.6 KiB
R
86 lines
4.6 KiB
R
# if you need a new package, you should add it with renv::install(package) so your renv venv is updated
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library(RMariaDB)
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library(yaml)
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#' @description
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#' Auxiliary function to parse the connection credentials from a specifc group in ./credentials.yaml
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#' You can reause most of this function if you are connection to a DB or Web API.
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#' It's OK to delete this function if you don't need credentials, e.g., you are pulling data from a CSV for example.
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#' @param group the yaml key containing the credentials to connect to a database
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#' @preturn dbEngine a database engine (connection) ready to perform queries
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get_db_engine <- function(group){
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# The working dir is aways RAPIDS root folder, so your credentials file is always /credentials.yaml
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credentials <- read_yaml("./credentials.yaml")
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if(!group %in% names(credentials))
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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?"))
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dbEngine <- dbConnect(MariaDB(), db = credentials[[group]][["database"]],
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username = credentials[[group]][["user"]],
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password = credentials[[group]][["password"]],
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host = credentials[[group]][["host"]],
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port = credentials[[group]][["port"]])
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return(dbEngine)
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}
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# This file gets executed for each PHONE_SENSOR of each participant
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# If you are connecting to a database the env file containing its credentials is available at "./.env"
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# 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
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# You are not bound to databases or files, you can query a web API or whatever data source you need.
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#' @description
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#' RAPIDS allows users to use the keyword "infer" (previously "multiple") to automatically infer the mobile Operative System a device was running.
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#' 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.
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#'
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#' 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,
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#' and they have to assign the OS manually in the participant file
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @return The OS the device ran, "android" or "ios"
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infer_device_os <- function(stream_parameters, device){
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dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
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query <- paste0("SELECT device_id,brand FROM aware_device WHERE device_id = '", device, "'")
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message(paste0("Executing the following query to infer phone OS: ", query))
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os <- dbGetQuery(dbEngine, query)
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dbDisconnect(dbEngine)
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if(nrow(os) > 0)
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return(os %>% mutate(os = ifelse(brand == "iPhone", "ios", "android")) %>% pull(os))
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else
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stop(paste("We cannot infer the OS of the following device id because it does not exist in the aware_device table:", device))
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return(os)
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}
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#' @description
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#' Gets the sensor data for a specific device id from a database table, file or whatever source you want to query
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#'
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#' @param stream_parameters The PHONE_STREAM_PARAMETERS key in config.yaml. If you need specific parameters add them there.
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#' @param device A device ID string
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#' @param sensor_container database table or file containing the sensor data for all participants. This is the PHONE_SENSOR[CONTAINER] key in config.yaml
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#' @param columns the columns needed from this sensor (we recommend to only return these columns instead of every column in sensor_container)
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#' @return A dataframe with the sensor data for device
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pull_data <- function(stream_parameters, device, sensor, sensor_container, columns){
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dbEngine <- get_db_engine(stream_parameters$DATABASE_GROUP)
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select_items <- c()
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for (column in columns) {
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select_items <- append(select_items, paste0("data->>'$.", column, "' ", column))
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}
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query <- paste0("SELECT ", paste(select_items, collapse = ",")," FROM ", sensor_container, " WHERE ", columns$DEVICE_ID ," = '", device,"'")
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# Letting the user know what we are doing
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message(paste0("Executing the following query to download data: ", query))
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sensor_data <- dbGetQuery(dbEngine, query)
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dbDisconnect(dbEngine)
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if(nrow(sensor_data) == 0)
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warning(paste("The device '", device,"' did not have data in ", sensor_container))
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return(sensor_data)
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}
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